One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1)																		; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -wkATTGCACAAywh ; Alignment reference a 0 1173 857 3161 3 5 52 3 4369 17 4506 4512 149 1831 1226 c 0 816 719 307 3 4 3 4509 16 4467 9 3 2623 988 1193 g 0 861 1532 915 4 3 4418 2 107 5 4 3 337 502 930 t 0 1671 1413 138 4511 4509 48 7 29 32 2 3 1412 1200 1172
MA0102.3_shift3 (CEBPA)		0.947	0.744	10.183	0.730	0.946	0.701	0.968	2	3	2	4	2	2	2	2.429	1	; oligos_7nt_mkv5_m1 versus MA0102.3 (CEBPA); m=1/6; ncol2=11; w=11; offset=2; strand=D; shift=3; score= 2.4286; ---aTTGCAyAAym- ; cor=0.947; Ncor=0.744; logoDP=10.183; NIcor=0.730; NsEucl=0.946; SSD=0.701; NSW=0.968; rcor=2; rNcor=3; rlogoDP=2; rNIcor=4; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.429; match_rank=1 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0466.1_shift2 (CEBPB)		0.919	0.722	9.948	0.704	0.936	0.995	0.955	6	7	8	7	5	8	5	6.571	2	; oligos_7nt_mkv5_m1 versus MA0466.1 (CEBPB); m=2/6; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 6.5714; --kATTGCAymAy-- ; cor=0.919; Ncor=0.722; logoDP=9.948; NIcor=0.704; NsEucl=0.936; SSD=0.995; NSW=0.955; rcor=6; rNcor=7; rlogoDP=8; rNIcor=7; rNsEucl=5; rSSD=8; rNSW=5; rank_mean=6.571; match_rank=2 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0133.1_shift8 (BRCA1)		0.841	0.421	3.257	0.425	0.903	0.920	0.934	40	113	80	59	57	6	14	52.714	46	; oligos_7nt_mkv5_m1 versus MA0133.1 (BRCA1); m=3/6; ncol2=7; w=7; offset=7; strand=D; shift=8; score=52.7143; --------mCAAcms ; cor=0.841; Ncor=0.421; logoDP=3.257; NIcor=0.425; NsEucl=0.903; SSD=0.920; NSW=0.934; rcor=40; rNcor=113; rlogoDP=80; rNIcor=59; rNsEucl=57; rSSD=6; rNSW=14; rank_mean=52.714; match_rank=46 a 0 0 0 0 0 0 0 0 15 4 41 36 7 19 3 c 0 0 0 0 0 0 0 0 11 35 1 2 29 14 22 g 0 0 0 0 0 0 0 0 10 2 1 4 6 7 15 t 0 0 0 0 0 0 0 0 7 2 0 1 1 3 3
MA0102.1_rc_shift0 (Cebpa_rc)		0.824	0.604	0.206	-0.158	0.908	2.040	0.907	56	44	123	115	40	67	48	70.429	69	; oligos_7nt_mkv5_m1 versus MA0102.1_rc (Cebpa_rc); m=4/6; ncol2=12; w=11; offset=-1; strand=R; shift=0; score=70.4286; vrbrTTGcrmaA--- ; cor=0.824; Ncor=0.604; logoDP=0.206; NIcor=-0.158; NsEucl=0.908; SSD=2.040; NSW=0.907; rcor=56; rNcor=44; rlogoDP=123; rNIcor=115; rNsEucl=40; rSSD=67; rNSW=48; rank_mean=70.429; match_rank=69 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.2_rc_shift3 (CEBPA_rc)		0.838	0.539	2.636	0.051	0.891	1.910	0.894	44	74	95	93	94	57	76	76.143	82	; oligos_7nt_mkv5_m1 versus MA0102.2_rc (CEBPA_rc); m=5/6; ncol2=9; w=9; offset=2; strand=R; shift=3; score=76.1429; ---rTTGcrmaA--- ; cor=0.838; Ncor=0.539; logoDP=2.636; NIcor=0.051; NsEucl=0.891; SSD=1.910; NSW=0.894; rcor=44; rNcor=74; rlogoDP=95; rNIcor=93; rNsEucl=94; rSSD=57; rNSW=76; rank_mean=76.143; match_rank=82 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0078.1_rc_shift7 (Sox17_rc)		0.758	0.405	2.129	0.068	0.879	1.876	0.883	115	122	104	89	115	56	95	99.429	119	; oligos_7nt_mkv5_m1 versus MA0078.1_rc (Sox17_rc); m=6/6; ncol2=9; w=8; offset=6; strand=R; shift=7; score=99.4286; -------sACAATrd ; cor=0.758; Ncor=0.405; logoDP=2.129; NIcor=0.068; NsEucl=0.879; SSD=1.876; NSW=0.883; rcor=115; rNcor=122; rlogoDP=104; rNIcor=89; rNsEucl=115; rSSD=56; rNSW=95; rank_mean=99.429; match_rank=119 a 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 c 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 g 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 t 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)																		; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; atGATTGCACAACwy ; Alignment reference a 1046 663 145 2141 1 1 72 6 2545 94 2687 2687 42 1152 677 c 471 240 158 56 4 1 6 2698 51 2522 26 10 2208 613 803 g 578 483 2160 474 4 10 2428 2 31 16 1 9 95 166 539 t 620 1329 252 44 2706 2703 209 9 88 83 1 9 370 784 696
MA0102.3_shift3 (CEBPA)		0.936	0.687	9.852	0.673	0.942	0.821	0.963	3	14	10	12	4	5	4	7.429	3	; oligos_6nt_mkv4_m5 versus MA0102.3 (CEBPA); m=1/5; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 7.4286; ---aTTGCAyAAym- ; cor=0.936; Ncor=0.687; logoDP=9.852; NIcor=0.673; NsEucl=0.942; SSD=0.821; NSW=0.963; rcor=3; rNcor=14; rlogoDP=10; rNIcor=12; rNsEucl=4; rSSD=5; rNSW=4; rank_mean=7.429; match_rank=3 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0466.1_shift2 (CEBPB)		0.887	0.650	9.694	0.629	0.923	1.445	0.934	10	25	15	21	12	25	13	17.286	5	; oligos_6nt_mkv4_m5 versus MA0466.1 (CEBPB); m=2/5; ncol2=11; w=11; offset=2; strand=D; shift=2; score=17.2857; --kATTGCAymAy-- ; cor=0.887; Ncor=0.650; logoDP=9.694; NIcor=0.629; NsEucl=0.923; SSD=1.445; NSW=0.934; rcor=10; rNcor=25; rlogoDP=15; rNIcor=21; rNsEucl=12; rSSD=25; rNSW=13; rank_mean=17.286; match_rank=5 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0133.1_shift8 (BRCA1)		0.871	0.406	3.115	0.410	0.910	0.792	0.943	19	120	83	63	36	4	8	47.571	37	; oligos_6nt_mkv4_m5 versus MA0133.1 (BRCA1); m=3/5; ncol2=7; w=7; offset=8; strand=D; shift=8; score=47.5714; --------mCAAcms ; cor=0.871; Ncor=0.406; logoDP=3.115; NIcor=0.410; NsEucl=0.910; SSD=0.792; NSW=0.943; rcor=19; rNcor=120; rlogoDP=83; rNIcor=63; rNsEucl=36; rSSD=4; rNSW=8; rank_mean=47.571; match_rank=37 a 0 0 0 0 0 0 0 0 15 4 41 36 7 19 3 c 0 0 0 0 0 0 0 0 11 35 1 2 29 14 22 g 0 0 0 0 0 0 0 0 10 2 1 4 6 7 15 t 0 0 0 0 0 0 0 0 7 2 0 1 1 3 3
MA0102.2_rc_shift3 (CEBPA_rc)		0.843	0.506	2.643	0.048	0.895	1.772	0.902	37	86	93	95	82	45	60	71.143	70	; oligos_6nt_mkv4_m5 versus MA0102.2_rc (CEBPA_rc); m=4/5; ncol2=9; w=9; offset=3; strand=R; shift=3; score=71.1429; ---rTTGcrmaA--- ; cor=0.843; Ncor=0.506; logoDP=2.643; NIcor=0.048; NsEucl=0.895; SSD=1.772; NSW=0.902; rcor=37; rNcor=86; rlogoDP=93; rNIcor=95; rNsEucl=82; rSSD=45; rNSW=60; rank_mean=71.143; match_rank=70 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.1_rc_shift0 (Cebpa_rc)		0.802	0.641	0.296	-0.164	0.910	2.329	0.903	79	30	119	117	37	90	56	75.429	79	; oligos_6nt_mkv4_m5 versus MA0102.1_rc (Cebpa_rc); m=5/5; ncol2=12; w=12; offset=0; strand=R; shift=0; score=75.4286; vrbrTTGcrmaA--- ; cor=0.802; Ncor=0.641; logoDP=0.296; NIcor=-0.164; NsEucl=0.910; SSD=2.329; NSW=0.903; rcor=79; rNcor=30; rlogoDP=119; rNIcor=117; rNsEucl=37; rSSD=90; rNSW=56; rank_mean=75.429; match_rank=79 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m1_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
oligos_8nt_mkv6_m1_shift0 (oligos_8nt_mkv6_m1)																		; oligos_8nt_mkv6_m1; m=0 (reference); ncol1=15; shift=0; ncol=16; atGGTTGCACAATah- ; Alignment reference a 916 519 193 371 2 4 54 1 2146 57 2247 2242 18 885 631 0 c 427 233 24 77 4 0 3 2252 32 2134 18 4 475 510 578 0 g 477 406 1804 1760 2 8 2128 5 32 14 0 14 49 354 370 0 t 447 1109 246 59 2259 2255 82 9 57 62 2 7 1725 518 688 0
MA0102.3_shift3 (CEBPA)		0.905	0.664	9.835	0.645	0.931	1.166	0.947	8	19	11	18	7	15	7	12.143	4	; oligos_8nt_mkv6_m1 versus MA0102.3 (CEBPA); m=1/6; ncol2=11; w=11; offset=3; strand=D; shift=3; score=12.1429; ---aTTGCAyAAym-- ; cor=0.905; Ncor=0.664; logoDP=9.835; NIcor=0.645; NsEucl=0.931; SSD=1.166; NSW=0.947; rcor=8; rNcor=19; rlogoDP=11; rNIcor=18; rNsEucl=7; rSSD=15; rNSW=7; rank_mean=12.143; match_rank=4 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0466.1_shift2 (CEBPB)		0.857	0.629	9.666	0.600	0.914	1.791	0.919	27	34	17	27	27	48	35	30.714	16	; oligos_8nt_mkv6_m1 versus MA0466.1 (CEBPB); m=2/6; ncol2=11; w=11; offset=2; strand=D; shift=2; score=30.7143; --kATTGCAymAy--- ; cor=0.857; Ncor=0.629; logoDP=9.666; NIcor=0.600; NsEucl=0.914; SSD=1.791; NSW=0.919; rcor=27; rNcor=34; rlogoDP=17; rNIcor=27; rNsEucl=27; rSSD=48; rNSW=35; rank_mean=30.714; match_rank=16 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0078.1_rc_shift7 (Sox17_rc)		0.854	0.427	2.638	0.134	0.906	1.140	0.929	30	107	94	81	48	13	19	56.000	48	; oligos_8nt_mkv6_m1 versus MA0078.1_rc (Sox17_rc); m=3/6; ncol2=9; w=8; offset=7; strand=R; shift=7; score= 56; -------sACAATrdr ; cor=0.854; Ncor=0.427; logoDP=2.638; NIcor=0.134; NsEucl=0.906; SSD=1.140; NSW=0.929; rcor=30; rNcor=107; rlogoDP=94; rNIcor=81; rNsEucl=48; rSSD=13; rNSW=19; rank_mean=56.000; match_rank=48 a 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 c 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 g 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 t 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7
MA0102.2_shift4 (CEBPA)		0.819	0.492	6.238	0.466	0.889	2.012	0.888	58	92	56	54	101	64	88	73.286	75	; oligos_8nt_mkv6_m1 versus MA0102.2 (CEBPA); m=4/6; ncol2=9; w=9; offset=4; strand=D; shift=4; score=73.2857; ----TtkygCAAy--- ; cor=0.819; Ncor=0.492; logoDP=6.238; NIcor=0.466; NsEucl=0.889; SSD=2.012; NSW=0.888; rcor=58; rNcor=92; rlogoDP=56; rNIcor=54; rNsEucl=101; rSSD=64; rNSW=88; rank_mean=73.286; match_rank=75 a 0 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
MA0043.1_shift2 (HLF)		0.753	0.602	6.217	0.584	0.899	2.942	0.877	119	45	59	29	71	121	104	78.286	87	; oligos_8nt_mkv6_m1 versus MA0043.1 (HLF); m=5/6; ncol2=12; w=12; offset=2; strand=D; shift=2; score=78.2857; --krTTACryAAth-- ; cor=0.753; Ncor=0.602; logoDP=6.217; NIcor=0.584; NsEucl=0.899; SSD=2.942; NSW=0.877; rcor=119; rNcor=45; rlogoDP=59; rNIcor=29; rNsEucl=71; rSSD=121; rNSW=104; rank_mean=78.286; match_rank=87 a 0 0 1 6 1 0 13 0 6 0 13 15 2 5 0 0 c 0 0 4 0 0 0 1 15 0 9 4 0 3 5 0 0 g 0 0 8 12 0 3 2 1 12 0 1 1 1 3 0 0 t 0 0 5 0 17 15 2 2 0 9 0 2 12 5 0 0
MA0102.1_rc_shift0 (Cebpa_rc)		0.771	0.617	0.293	-0.165	0.904	2.655	0.889	102	38	120	118	54	114	86	90.286	109	; oligos_8nt_mkv6_m1 versus MA0102.1_rc (Cebpa_rc); m=6/6; ncol2=12; w=12; offset=0; strand=R; shift=0; score=90.2857; vrbrTTGcrmaA---- ; cor=0.771; Ncor=0.617; logoDP=0.293; NIcor=-0.165; NsEucl=0.904; SSD=2.655; NSW=0.889; rcor=102; rNcor=38; rlogoDP=120; rNIcor=118; rNsEucl=54; rSSD=114; rNSW=86; rank_mean=90.286; match_rank=109 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_8nt_mkv6_m4_shift1 (oligos_8nt_mkv6_m4)																		; oligos_8nt_mkv6_m4; m=0 (reference); ncol1=13; shift=1; ncol=14; -wrTTACACAATah ; Alignment reference a 0 768 1278 9 3 2545 2 2026 1 2529 2545 143 934 674 c 0 372 377 3 0 0 2552 7 2516 4 1 447 595 648 g 0 562 670 8 10 10 2 516 0 21 8 179 403 433 t 0 862 239 2544 2551 9 8 15 47 10 10 1795 632 809
MA0043.1_shift1 (HLF)		0.856	0.791	6.300	0.768	0.925	1.604	0.933	28	2	49	2	8	31	15	19.286	6	; oligos_8nt_mkv6_m4 versus MA0043.1 (HLF); m=1/7; ncol2=12; w=12; offset=0; strand=D; shift=1; score=19.2857; -krTTACryAAth- ; cor=0.856; Ncor=0.791; logoDP=6.300; NIcor=0.768; NsEucl=0.925; SSD=1.604; NSW=0.933; rcor=28; rNcor=2; rlogoDP=49; rNIcor=2; rNsEucl=8; rSSD=31; rNSW=15; rank_mean=19.286; match_rank=6 a 0 1 6 1 0 13 0 6 0 13 15 2 5 0 c 0 4 0 0 0 1 15 0 9 4 0 3 5 0 g 0 8 12 0 3 2 1 12 0 1 1 1 3 0 t 0 5 0 17 15 2 2 0 9 0 2 12 5 0
MA0102.3_shift2 (CEBPA)		0.810	0.686	9.050	0.681	0.907	2.083	0.905	71	15	29	11	44	70	53	41.857	27	; oligos_8nt_mkv6_m4 versus MA0102.3 (CEBPA); m=2/7; ncol2=11; w=11; offset=1; strand=D; shift=2; score=41.8571; --aTTGCAyAAym- ; cor=0.810; Ncor=0.686; logoDP=9.050; NIcor=0.681; NsEucl=0.907; SSD=2.083; NSW=0.905; rcor=71; rNcor=15; rlogoDP=29; rNIcor=11; rNsEucl=44; rSSD=70; rNSW=53; rank_mean=41.857; match_rank=27 a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0102.1_shift3 (Cebpa)		0.807	0.634	6.278	0.610	0.908	2.061	0.906	73	31	50	22	43	69	52	48.571	39	; oligos_8nt_mkv6_m4 versus MA0102.1 (Cebpa); m=3/7; ncol2=12; w=11; offset=2; strand=D; shift=3; score=48.5714; ---TtkygCAAyvy ; cor=0.807; Ncor=0.634; logoDP=6.278; NIcor=0.610; NsEucl=0.908; SSD=2.061; NSW=0.906; rcor=73; rNcor=31; rlogoDP=50; rNIcor=22; rNsEucl=43; rSSD=69; rNSW=52; rank_mean=48.571; match_rank=39 a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 t 0 0 0 15 12 7 5 2 1 0 0 10 2 8
MA0466.1_shift1 (CEBPB)		0.784	0.663	8.817	0.653	0.901	2.373	0.892	88	20	32	16	64	94	79	56.143	49	; oligos_8nt_mkv6_m4 versus MA0466.1 (CEBPB); m=4/7; ncol2=11; w=11; offset=0; strand=D; shift=1; score=56.1429; -kATTGCAymAy-- ; cor=0.784; Ncor=0.663; logoDP=8.817; NIcor=0.653; NsEucl=0.901; SSD=2.373; NSW=0.892; rcor=88; rNcor=20; rlogoDP=32; rNIcor=16; rNsEucl=64; rSSD=94; rNSW=79; rank_mean=56.143; match_rank=49 a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0078.1_rc_shift6 (Sox17_rc)		0.837	0.479	2.335	0.155	0.902	1.226	0.923	45	98	101	75	59	17	26	60.143	57	; oligos_8nt_mkv6_m4 versus MA0078.1_rc (Sox17_rc); m=5/7; ncol2=9; w=8; offset=5; strand=R; shift=6; score=60.1429; ------sACAATrd ; cor=0.837; Ncor=0.479; logoDP=2.335; NIcor=0.155; NsEucl=0.902; SSD=1.226; NSW=0.923; rcor=45; rNcor=98; rlogoDP=101; rNIcor=75; rNsEucl=59; rSSD=17; rNSW=26; rank_mean=60.143; match_rank=57 a 0 0 0 0 0 0 4 29 0 31 30 1 9 11 c 0 0 0 0 0 0 10 2 31 0 0 0 1 4 g 0 0 0 0 0 0 17 0 0 0 1 0 18 8 t 0 0 0 0 0 0 0 0 0 0 0 30 3 8
MA0102.2_shift3 (CEBPA)		0.817	0.566	6.276	0.537	0.890	1.970	0.891	60	62	51	38	98	61	83	64.714	63	; oligos_8nt_mkv6_m4 versus MA0102.2 (CEBPA); m=6/7; ncol2=9; w=9; offset=2; strand=D; shift=3; score=64.7143; ---TtkygCAAy-- ; cor=0.817; Ncor=0.566; logoDP=6.276; NIcor=0.537; NsEucl=0.890; SSD=1.970; NSW=0.891; rcor=60; rNcor=62; rlogoDP=51; rNIcor=38; rNsEucl=98; rSSD=61; rNSW=83; rank_mean=64.714; match_rank=63 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0
MA0025.1_rc_shift0 (NFIL3_rc)		0.812	0.580	1.804	0.055	0.899	2.039	0.898	67	53	108	92	70	66	69	75.000	77	; oligos_8nt_mkv6_m4 versus MA0025.1_rc (NFIL3_rc); m=7/7; ncol2=11; w=10; offset=-1; strand=R; shift=0; score= 75; ayrTTACrTAA--- ; cor=0.812; Ncor=0.580; logoDP=1.804; NIcor=0.055; NsEucl=0.899; SSD=2.039; NSW=0.898; rcor=67; rNcor=53; rlogoDP=108; rNIcor=92; rNsEucl=70; rSSD=66; rNSW=69; rank_mean=75.000; match_rank=77 a 10 4 8 0 0 23 0 15 1 21 22 0 0 0 c 3 7 4 1 0 0 21 0 0 2 0 0 0 0 g 5 5 11 0 0 0 0 8 0 0 0 0 0 0 t 5 7 0 22 23 0 2 0 22 0 1 0 0 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_8nt_m1_shift0 (positions_8nt_m1)																		; positions_8nt_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; amAGATTGCAAAACww ; Alignment reference a 172 182 482 52 497 2 2 12 3 517 451 522 535 8 215 163 c 112 161 5 27 15 3 0 2 539 6 70 25 3 479 124 119 g 134 132 23 439 22 2 2 518 5 15 2 2 7 22 43 128 t 131 74 39 31 15 542 545 17 2 11 26 0 4 40 167 139
MA0102.3_shift4 (CEBPA)		0.888	0.610	9.440	0.600	0.925	1.358	0.938	9	41	22	28	9	19	10	19.714	7	; positions_8nt_m1 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=4; strand=D; shift=4; score=19.7143; ----aTTGCAyAAym- ; cor=0.888; Ncor=0.610; logoDP=9.440; NIcor=0.600; NsEucl=0.925; SSD=1.358; NSW=0.938; rcor=9; rNcor=41; rlogoDP=22; rNIcor=28; rNsEucl=9; rSSD=19; rNSW=10; rank_mean=19.714; match_rank=7 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0466.1_shift3 (CEBPB)		0.828	0.569	9.326	0.559	0.906	2.128	0.903	53	58	25	30	45	74	54	48.429	38	; positions_8nt_m1 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=3; strand=D; shift=3; score=48.4286; ---kATTGCAymAy-- ; cor=0.828; Ncor=0.569; logoDP=9.326; NIcor=0.559; NsEucl=0.906; SSD=2.128; NSW=0.903; rcor=53; rNcor=58; rlogoDP=25; rNIcor=30; rNsEucl=45; rSSD=74; rNSW=54; rank_mean=48.429; match_rank=38 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0102.2_rc_shift4 (CEBPA_rc)		0.861	0.484	3.266	0.135	0.901	1.596	0.911	23	95	79	80	65	30	42	59.143	55	; positions_8nt_m1 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=4; strand=R; shift=4; score=59.1429; ----rTTGcrmaA--- ; cor=0.861; Ncor=0.484; logoDP=3.266; NIcor=0.135; NsEucl=0.901; SSD=1.596; NSW=0.911; rcor=23; rNcor=95; rlogoDP=79; rNIcor=80; rNsEucl=65; rSSD=30; rNSW=42; rank_mean=59.143; match_rank=55 a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.1_rc_shift1 (Cebpa_rc)		0.833	0.625	0.301	-0.199	0.913	2.200	0.908	48	35	118	122	34	80	47	69.143	67	; positions_8nt_m1 versus MA0102.1_rc (Cebpa_rc); m=4/4; ncol2=12; w=12; offset=1; strand=R; shift=1; score=69.1429; -vrbrTTGcrmaA--- ; cor=0.833; Ncor=0.625; logoDP=0.301; NIcor=-0.199; NsEucl=0.913; SSD=2.200; NSW=0.908; rcor=48; rNcor=35; rlogoDP=118; rNIcor=122; rNsEucl=34; rSSD=80; rNSW=47; rank_mean=69.143; match_rank=67 a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)																		; positions_7nt_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; rmAGATTGCACAACTyt ; Alignment reference a 94 132 260 16 314 0 0 10 2 311 7 331 333 6 35 67 73 c 71 85 4 10 5 0 0 0 330 11 318 3 0 296 15 105 76 g 95 77 9 277 13 1 2 309 1 1 1 0 0 7 2 77 54 t 74 40 61 31 2 333 332 15 1 11 8 0 1 25 282 85 131
MA0102.3_shift4 (CEBPA)		0.886	0.573	10.155	0.557	0.919	1.591	0.928	11	55	4	31	16	29	21	23.857	8	; positions_7nt_m2 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=4; strand=D; shift=4; score=23.8571; ----aTTGCAyAAym-- ; cor=0.886; Ncor=0.573; logoDP=10.155; NIcor=0.557; NsEucl=0.919; SSD=1.591; NSW=0.928; rcor=11; rNcor=55; rlogoDP=4; rNIcor=31; rNsEucl=16; rSSD=29; rNSW=21; rank_mean=23.857; match_rank=8 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0466.1_shift3 (CEBPB)		0.875	0.566	10.062	0.546	0.916	1.713	0.922	16	61	5	35	21	38	27	29.000	12	; positions_7nt_m2 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 29; ---kATTGCAymAy--- ; cor=0.875; Ncor=0.566; logoDP=10.062; NIcor=0.546; NsEucl=0.916; SSD=1.713; NSW=0.922; rcor=16; rNcor=61; rlogoDP=5; rNIcor=35; rNsEucl=21; rSSD=38; rNSW=27; rank_mean=29.000; match_rank=12 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0102.1_rc_shift1 (Cebpa_rc)		0.811	0.572	0.356	-0.184	0.906	2.540	0.894	69	56	115	119	46	105	74	83.429	98	; positions_7nt_m2 versus MA0102.1_rc (Cebpa_rc); m=3/4; ncol2=12; w=12; offset=1; strand=R; shift=1; score=83.4286; -vrbrTTGcrmaA---- ; cor=0.811; Ncor=0.572; logoDP=0.356; NIcor=-0.184; NsEucl=0.906; SSD=2.540; NSW=0.894; rcor=69; rNcor=56; rlogoDP=115; rNIcor=119; rNsEucl=46; rSSD=105; rNSW=74; rank_mean=83.429; match_rank=98 a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 0 c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 0 g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 0 t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0 0
MA0102.2_rc_shift4 (CEBPA_rc)		0.835	0.442	2.716	0.036	0.890	1.972	0.890	47	103	90	99	99	62	85	83.571	99	; positions_7nt_m2 versus MA0102.2_rc (CEBPA_rc); m=4/4; ncol2=9; w=9; offset=4; strand=R; shift=4; score=83.5714; ----rTTGcrmaA---- ; cor=0.835; Ncor=0.442; logoDP=2.716; NIcor=0.036; NsEucl=0.890; SSD=1.972; NSW=0.890; rcor=47; rNcor=103; rlogoDP=90; rNIcor=99; rNsEucl=99; rSSD=62; rNSW=85; rank_mean=83.571; match_rank=99 a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 0 c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 0 g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 0 t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift0 ; 5 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m5_shift0 (positions_7nt_m5)																		; positions_7nt_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; wmACATTGCACAACTsy ; Alignment reference a 73 84 193 16 219 0 0 4 0 221 11 226 224 2 20 52 44 c 48 64 6 163 4 0 0 0 227 3 213 1 0 205 12 64 62 g 45 44 16 18 0 0 3 206 0 1 1 0 1 4 0 58 48 t 62 36 13 31 5 228 225 18 1 3 3 1 3 17 196 54 74
MA0102.3_shift4 (CEBPA)		0.883	0.571	10.162	0.554	0.918	1.644	0.925	12	57	3	32	19	34	24	25.857	9	; positions_7nt_m5 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=4; strand=D; shift=4; score=25.8571; ----aTTGCAyAAym-- ; cor=0.883; Ncor=0.571; logoDP=10.162; NIcor=0.554; NsEucl=0.918; SSD=1.644; NSW=0.925; rcor=12; rNcor=57; rlogoDP=3; rNIcor=32; rNsEucl=19; rSSD=34; rNSW=24; rank_mean=25.857; match_rank=9 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0466.1_shift3 (CEBPB)		0.855	0.553	10.041	0.543	0.911	1.913	0.913	29	66	6	36	35	58	40	38.571	23	; positions_7nt_m5 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=3; strand=D; shift=3; score=38.5714; ---kATTGCAymAy--- ; cor=0.855; Ncor=0.553; logoDP=10.041; NIcor=0.543; NsEucl=0.911; SSD=1.913; NSW=0.913; rcor=29; rNcor=66; rlogoDP=6; rNIcor=36; rNsEucl=35; rSSD=58; rNSW=40; rank_mean=38.571; match_rank=23 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0102.2_rc_shift4 (CEBPA_rc)		0.829	0.439	2.792	0.031	0.888	2.029	0.887	50	104	89	101	102	65	90	85.857	101	; positions_7nt_m5 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=4; strand=R; shift=4; score=85.8571; ----rTTGcrmaA---- ; cor=0.829; Ncor=0.439; logoDP=2.792; NIcor=0.031; NsEucl=0.888; SSD=2.029; NSW=0.887; rcor=50; rNcor=104; rlogoDP=89; rNIcor=101; rNsEucl=102; rSSD=65; rNSW=90; rank_mean=85.857; match_rank=101 a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 0 c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 0 g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 0 t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0 0
MA0102.1_rc_shift1 (Cebpa_rc)		0.805	0.568	0.267	-0.193	0.906	2.565	0.893	77	59	122	121	49	108	78	87.714	106	; positions_7nt_m5 versus MA0102.1_rc (Cebpa_rc); m=4/4; ncol2=12; w=12; offset=1; strand=R; shift=1; score=87.7143; -vrbrTTGcrmaA---- ; cor=0.805; Ncor=0.568; logoDP=0.267; NIcor=-0.193; NsEucl=0.906; SSD=2.565; NSW=0.893; rcor=77; rNcor=59; rlogoDP=122; rNIcor=121; rNsEucl=49; rSSD=108; rNSW=78; rank_mean=87.714; match_rank=106 a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 0 c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 0 g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 0 t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)																		; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=15; shift=1; ncol=16; -dkATTGTGCAATCwt ; Alignment reference a 0 1017 719 2822 11 5 121 129 5 243 3289 3292 59 474 1377 760 c 0 520 532 95 7 0 18 37 1 2929 18 4 304 2259 685 751 g 0 845 848 350 11 35 3067 63 3295 7 1 5 76 297 337 623 t 0 927 1210 42 3280 3269 103 3080 8 130 1 8 2870 279 910 1175
MA0102.3_rc_shift2 (CEBPA_rc)		0.948	0.695	4.203	0.060	0.946	0.706	0.968	1	11	72	91	3	3	3	26.286	10	; oligos_6nt_mkv4_m1 versus MA0102.3_rc (CEBPA_rc); m=1/5; ncol2=11; w=11; offset=1; strand=R; shift=2; score=26.2857; --krTTrTGCAAt--- ; cor=0.948; Ncor=0.695; logoDP=4.203; NIcor=0.060; NsEucl=0.946; SSD=0.706; NSW=0.968; rcor=1; rNcor=11; rlogoDP=72; rNIcor=91; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=26.286; match_rank=10 a 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 c 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 g 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 t 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0
MA0466.1_rc_shift3 (CEBPB_rc)		0.924	0.678	2.822	-0.039	0.935	1.011	0.954	4	17	88	105	6	9	6	33.571	20	; oligos_6nt_mkv4_m1 versus MA0466.1_rc (CEBPB_rc); m=2/5; ncol2=11; w=11; offset=2; strand=R; shift=3; score=33.5714; ---rTkrTGCAATm-- ; cor=0.924; Ncor=0.678; logoDP=2.822; NIcor=-0.039; NsEucl=0.935; SSD=1.011; NSW=0.954; rcor=4; rNcor=17; rlogoDP=88; rNIcor=105; rNsEucl=6; rSSD=9; rNSW=6; rank_mean=33.571; match_rank=20 a 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 c 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 g 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 t 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0
MA0078.1_shift0 (Sox17)		0.861	0.431	6.883	0.426	0.908	1.089	0.932	24	106	39	58	42	11	17	42.429	29	; oligos_6nt_mkv4_m1 versus MA0078.1 (Sox17); m=3/5; ncol2=9; w=8; offset=-1; strand=D; shift=0; score=42.4286; yhyATTGTs------- ; cor=0.861; Ncor=0.431; logoDP=6.883; NIcor=0.426; NsEucl=0.908; SSD=1.089; NSW=0.932; rcor=24; rNcor=106; rlogoDP=39; rNIcor=58; rNsEucl=42; rSSD=11; rNSW=17; rank_mean=42.429; match_rank=29 a 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 0 c 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 0 g 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 0 t 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0 0
MA0102.1_shift4 (Cebpa)		0.811	0.649	6.237	0.631	0.913	2.194	0.909	68	27	57	20	33	79	46	47.143	36	; oligos_6nt_mkv4_m1 versus MA0102.1 (Cebpa); m=4/5; ncol2=12; w=12; offset=3; strand=D; shift=4; score=47.1429; ----TtkygCAAyvyb ; cor=0.811; Ncor=0.649; logoDP=6.237; NIcor=0.631; NsEucl=0.913; SSD=2.194; NSW=0.909; rcor=68; rNcor=27; rlogoDP=57; rNIcor=20; rNsEucl=33; rSSD=79; rNSW=46; rank_mean=47.143; match_rank=36 a 0 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
MA0102.2_shift4 (CEBPA)		0.839	0.503	6.225	0.480	0.894	1.837	0.898	43	89	58	52	88	53	70	64.714	62	; oligos_6nt_mkv4_m1 versus MA0102.2 (CEBPA); m=5/5; ncol2=9; w=9; offset=3; strand=D; shift=4; score=64.7143; ----TtkygCAAy--- ; cor=0.839; Ncor=0.503; logoDP=6.225; NIcor=0.480; NsEucl=0.894; SSD=1.837; NSW=0.898; rcor=43; rNcor=89; rlogoDP=58; rNIcor=52; rNsEucl=88; rSSD=53; rNSW=70; rank_mean=64.714; match_rank=62 a 0 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)																		; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; wtATTTCACAATCwy ; Alignment reference a 394 218 1344 6 10 132 6 1281 17 1366 1387 18 237 486 348 c 277 242 17 9 7 9 1392 26 1335 33 4 63 1048 300 369 g 313 341 33 4 46 166 3 48 5 1 6 13 43 155 231 t 419 602 9 1384 1340 1096 2 48 46 3 6 1309 75 462 455
MA0466.1_shift1 (CEBPB)		0.862	0.632	9.285	0.609	0.917	1.673	0.924	21	32	28	23	20	35	25	26.286	11	; positions_7nt_m1 versus MA0466.1 (CEBPB); m=1/5; ncol2=11; w=11; offset=1; strand=D; shift=1; score=26.2857; -kATTGCAymAy--- ; cor=0.862; Ncor=0.632; logoDP=9.285; NIcor=0.609; NsEucl=0.917; SSD=1.673; NSW=0.924; rcor=21; rNcor=32; rlogoDP=28; rNIcor=23; rNsEucl=20; rSSD=35; rNSW=25; rank_mean=26.286; match_rank=11 a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0102.3_shift2 (CEBPA)		0.858	0.629	9.288	0.601	0.914	1.799	0.918	26	33	27	26	29	49	36	32.286	18	; positions_7nt_m1 versus MA0102.3 (CEBPA); m=2/5; ncol2=11; w=11; offset=2; strand=D; shift=2; score=32.2857; --aTTGCAyAAym-- ; cor=0.858; Ncor=0.629; logoDP=9.288; NIcor=0.601; NsEucl=0.914; SSD=1.799; NSW=0.918; rcor=26; rNcor=33; rlogoDP=27; rNIcor=26; rNsEucl=29; rSSD=49; rNSW=36; rank_mean=32.286; match_rank=18 a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0102.1_shift3 (Cebpa)		0.813	0.650	6.099	0.632	0.914	2.138	0.911	65	24	61	19	28	75	43	45.000	33	; positions_7nt_m1 versus MA0102.1 (Cebpa); m=3/5; ncol2=12; w=12; offset=3; strand=D; shift=3; score= 45; ---TtkygCAAyvyb ; cor=0.813; Ncor=0.650; logoDP=6.099; NIcor=0.632; NsEucl=0.914; SSD=2.138; NSW=0.911; rcor=65; rNcor=24; rlogoDP=61; rNIcor=19; rNsEucl=28; rSSD=75; rNSW=43; rank_mean=45.000; match_rank=33 a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
MA0102.2_shift3 (CEBPA)		0.841	0.504	6.083	0.482	0.896	1.760	0.902	41	88	62	51	79	43	57	60.143	56	; positions_7nt_m1 versus MA0102.2 (CEBPA); m=4/5; ncol2=9; w=9; offset=3; strand=D; shift=3; score=60.1429; ---TtkygCAAy--- ; cor=0.841; Ncor=0.504; logoDP=6.083; NIcor=0.482; NsEucl=0.896; SSD=1.760; NSW=0.902; rcor=41; rNcor=88; rlogoDP=62; rNIcor=51; rNsEucl=79; rSSD=43; rNSW=57; rank_mean=60.143; match_rank=56 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
MA0078.1_rc_shift6 (Sox17_rc)		0.800	0.480	3.198	0.181	0.898	1.673	0.907	80	97	81	72	73	36	49	69.714	68	; positions_7nt_m1 versus MA0078.1_rc (Sox17_rc); m=5/5; ncol2=9; w=9; offset=6; strand=R; shift=6; score=69.7143; ------sACAATrdr ; cor=0.800; Ncor=0.480; logoDP=3.198; NIcor=0.181; NsEucl=0.898; SSD=1.673; NSW=0.907; rcor=80; rNcor=97; rlogoDP=81; rNIcor=72; rNsEucl=73; rSSD=36; rNSW=49; rank_mean=69.714; match_rank=68 a 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 c 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 g 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 t 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7

One-to-n matrix alignment; reference matrix: positions_8nt_m3_shift1 ; 5 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_8nt_m3_shift1 (positions_8nt_m3)																		; positions_8nt_m3; m=0 (reference); ncol1=14; shift=1; ncol=15; -wtATTGCCCAATaw ; Alignment reference a 0 331 246 842 1 1 12 2 34 5 1110 1118 50 412 284 c 0 229 210 94 0 1 0 1116 933 1097 4 0 179 259 273 g 0 247 258 141 0 1 1104 0 142 4 3 0 80 183 202 t 0 311 404 41 1117 1115 2 0 9 12 1 0 809 264 359
MA0102.3_shift3 (CEBPA)		0.844	0.663	9.783	0.657	0.913	1.814	0.918	36	21	12	15	31	51	38	29.143	13	; positions_8nt_m3 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=2; strand=D; shift=3; score=29.1429; ---aTTGCAyAAym- ; cor=0.844; Ncor=0.663; logoDP=9.783; NIcor=0.657; NsEucl=0.913; SSD=1.814; NSW=0.918; rcor=36; rNcor=21; rlogoDP=12; rNIcor=15; rNsEucl=31; rSSD=51; rNSW=38; rank_mean=29.143; match_rank=13 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0466.1_shift2 (CEBPB)		0.829	0.651	9.663	0.649	0.909	1.986	0.910	52	23	18	17	38	63	44	36.429	21	; positions_8nt_m3 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=1; strand=D; shift=2; score=36.4286; --kATTGCAymAy-- ; cor=0.829; Ncor=0.651; logoDP=9.663; NIcor=0.649; NsEucl=0.909; SSD=1.986; NSW=0.910; rcor=52; rNcor=23; rlogoDP=18; rNIcor=17; rNsEucl=38; rSSD=63; rNSW=44; rank_mean=36.429; match_rank=21 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0102.1_rc_shift0 (Cebpa_rc)		0.815	0.598	0.310	-0.156	0.908	2.048	0.907	61	48	117	114	41	68	50	71.286	71	; positions_8nt_m3 versus MA0102.1_rc (Cebpa_rc); m=3/4; ncol2=12; w=11; offset=-1; strand=R; shift=0; score=71.2857; vrbrTTGcrmaA--- ; cor=0.815; Ncor=0.598; logoDP=0.310; NIcor=-0.156; NsEucl=0.908; SSD=2.048; NSW=0.907; rcor=61; rNcor=48; rlogoDP=117; rNIcor=114; rNsEucl=41; rSSD=68; rNSW=50; rank_mean=71.286; match_rank=71 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.2_rc_shift3 (CEBPA_rc)		0.826	0.531	2.985	0.143	0.890	1.956	0.891	54	76	86	78	97	60	80	75.857	81	; positions_8nt_m3 versus MA0102.2_rc (CEBPA_rc); m=4/4; ncol2=9; w=9; offset=2; strand=R; shift=3; score=75.8571; ---rTTGcrmaA--- ; cor=0.826; Ncor=0.531; logoDP=2.985; NIcor=0.143; NsEucl=0.890; SSD=1.956; NSW=0.891; rcor=54; rNcor=76; rlogoDP=86; rNIcor=78; rNsEucl=97; rSSD=60; rNSW=80; rank_mean=75.857; match_rank=81 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0

One-to-n matrix alignment; reference matrix: positions_8nt_m4_shift0 ; 6 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_8nt_m4_shift0 (positions_8nt_m4)																		; positions_8nt_m4; m=0 (reference); ncol1=17; shift=0; ncol=17; raTGGTTGCACAAyAwt ; Alignment reference a 176 350 19 19 55 1 1 11 1 634 4 646 645 6 548 174 92 c 61 81 8 2 8 0 0 2 643 3 635 1 0 239 29 149 112 g 352 112 19 612 578 0 0 628 0 5 1 0 0 12 34 147 50 t 58 104 601 14 6 646 646 6 3 5 7 0 2 390 36 177 393
MA0102.3_shift4 (CEBPA)		0.872	0.564	10.262	0.542	0.916	1.725	0.922	17	63	1	37	23	40	29	30.000	14	; positions_8nt_m4 versus MA0102.3 (CEBPA); m=1/5; ncol2=11; w=11; offset=4; strand=D; shift=4; score= 30; ----aTTGCAyAAym-- ; cor=0.872; Ncor=0.564; logoDP=10.262; NIcor=0.542; NsEucl=0.916; SSD=1.725; NSW=0.922; rcor=17; rNcor=63; rlogoDP=1; rNIcor=37; rNsEucl=23; rSSD=40; rNSW=29; rank_mean=30.000; match_rank=14 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0466.1_shift3 (CEBPB)		0.825	0.534	10.032	0.501	0.902	2.334	0.894	55	75	7	46	61	91	77	58.857	54	; positions_8nt_m4 versus MA0466.1 (CEBPB); m=2/5; ncol2=11; w=11; offset=3; strand=D; shift=3; score=58.8571; ---kATTGCAymAy--- ; cor=0.825; Ncor=0.534; logoDP=10.032; NIcor=0.501; NsEucl=0.902; SSD=2.334; NSW=0.894; rcor=55; rNcor=75; rlogoDP=7; rNIcor=46; rNsEucl=61; rSSD=91; rNSW=77; rank_mean=58.857; match_rank=54 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0102.1_shift5 (Cebpa)		0.771	0.544	6.562	0.521	0.902	2.771	0.885	103	71	41	42	60	117	92	75.143	78	; positions_8nt_m4 versus MA0102.1 (Cebpa); m=3/5; ncol2=12; w=12; offset=5; strand=D; shift=5; score=75.1429; -----TtkygCAAyvyb ; cor=0.771; Ncor=0.544; logoDP=6.562; NIcor=0.521; NsEucl=0.902; SSD=2.771; NSW=0.885; rcor=103; rNcor=71; rlogoDP=41; rNIcor=42; rNsEucl=60; rSSD=117; rNSW=92; rank_mean=75.143; match_rank=78 a 0 0 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
MA0102.2_shift5 (CEBPA)		0.815	0.431	6.536	0.408	0.886	2.101	0.883	62	105	42	64	105	71	94	77.571	86	; positions_8nt_m4 versus MA0102.2 (CEBPA); m=4/5; ncol2=9; w=9; offset=5; strand=D; shift=5; score=77.5714; -----TtkygCAAy--- ; cor=0.815; Ncor=0.431; logoDP=6.536; NIcor=0.408; NsEucl=0.886; SSD=2.101; NSW=0.883; rcor=62; rNcor=105; rlogoDP=42; rNIcor=64; rNsEucl=105; rSSD=71; rNSW=94; rank_mean=77.571; match_rank=86 a 0 0 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
MA0078.1_rc_shift8 (Sox17_rc)		0.781	0.414	2.538	0.089	0.893	1.869	0.896	91	115	99	87	92	55	72	87.286	104	; positions_8nt_m4 versus MA0078.1_rc (Sox17_rc); m=5/5; ncol2=9; w=9; offset=8; strand=R; shift=8; score=87.2857; --------sACAATrdr ; cor=0.781; Ncor=0.414; logoDP=2.538; NIcor=0.089; NsEucl=0.893; SSD=1.869; NSW=0.896; rcor=91; rNcor=115; rlogoDP=99; rNIcor=87; rNsEucl=92; rSSD=55; rNSW=72; rank_mean=87.286; match_rank=104 a 0 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 c 0 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 g 0 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 t 0 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_8nt_mkv6_m2_shift1 (oligos_8nt_mkv6_m2)																		; oligos_8nt_mkv6_m2; m=0 (reference); ncol1=14; shift=1; ncol=15; -wkATTGTGAAATaw ; Alignment reference a 0 1308 894 3061 24 26 74 72 19 3238 3937 4012 92 1614 1207 c 0 658 553 238 10 9 14 263 2 359 63 6 333 982 869 g 0 987 1034 569 8 32 3924 36 3990 11 6 7 246 669 786 t 0 1082 1554 167 3993 3968 23 3664 24 427 29 10 3364 770 1173
MA0102.3_rc_shift2 (CEBPA_rc)		0.879	0.691	4.255	0.147	0.924	1.394	0.937	13	12	71	77	10	20	11	30.571	15	; oligos_8nt_mkv6_m2 versus MA0102.3_rc (CEBPA_rc); m=1/5; ncol2=11; w=11; offset=1; strand=R; shift=2; score=30.5714; --krTTrTGCAAt-- ; cor=0.879; Ncor=0.691; logoDP=4.255; NIcor=0.147; NsEucl=0.924; SSD=1.394; NSW=0.937; rcor=13; rNcor=12; rlogoDP=71; rNIcor=77; rNsEucl=10; rSSD=20; rNSW=11; rank_mean=30.571; match_rank=15 a 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 c 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 g 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 t 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0
MA0466.1_rc_shift3 (CEBPB_rc)		0.860	0.676	2.841	0.043	0.919	1.606	0.927	25	18	87	97	17	32	23	42.714	31	; oligos_8nt_mkv6_m2 versus MA0466.1_rc (CEBPB_rc); m=2/5; ncol2=11; w=11; offset=2; strand=R; shift=3; score=42.7143; ---rTkrTGCAATm- ; cor=0.860; Ncor=0.676; logoDP=2.841; NIcor=0.043; NsEucl=0.919; SSD=1.606; NSW=0.927; rcor=25; rNcor=18; rlogoDP=87; rNIcor=97; rNsEucl=17; rSSD=32; rNSW=23; rank_mean=42.714; match_rank=31 a 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 c 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 g 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 t 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0
MA0078.1_shift0 (Sox17)		0.852	0.454	6.708	0.449	0.905	1.144	0.929	31	102	40	57	51	14	20	45.000	32	; oligos_8nt_mkv6_m2 versus MA0078.1 (Sox17); m=3/5; ncol2=9; w=8; offset=-1; strand=D; shift=0; score= 45; yhyATTGTs------ ; cor=0.852; Ncor=0.454; logoDP=6.708; NIcor=0.449; NsEucl=0.905; SSD=1.144; NSW=0.929; rcor=31; rNcor=102; rlogoDP=40; rNIcor=57; rNsEucl=51; rSSD=14; rNSW=20; rank_mean=45.000; match_rank=32 a 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 c 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 g 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 t 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0
MA0102.2_rc_shift3 (CEBPA_rc)		0.850	0.547	3.146	0.175	0.900	1.625	0.910	32	70	82	74	69	33	45	57.857	51	; oligos_8nt_mkv6_m2 versus MA0102.2_rc (CEBPA_rc); m=4/5; ncol2=9; w=9; offset=2; strand=R; shift=3; score=57.8571; ---rTTGcrmaA--- ; cor=0.850; Ncor=0.547; logoDP=3.146; NIcor=0.175; NsEucl=0.900; SSD=1.625; NSW=0.910; rcor=32; rNcor=70; rlogoDP=82; rNIcor=74; rNsEucl=69; rSSD=33; rNSW=45; rank_mean=57.857; match_rank=51 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.1_rc_shift0 (Cebpa_rc)		0.840	0.616	0.284	-0.189	0.916	1.715	0.922	42	39	121	120	22	39	28	58.714	53	; oligos_8nt_mkv6_m2 versus MA0102.1_rc (Cebpa_rc); m=5/5; ncol2=12; w=11; offset=-1; strand=R; shift=0; score=58.7143; vrbrTTGcrmaA--- ; cor=0.840; Ncor=0.616; logoDP=0.284; NIcor=-0.189; NsEucl=0.916; SSD=1.715; NSW=0.922; rcor=42; rNcor=39; rlogoDP=121; rNIcor=120; rNsEucl=22; rSSD=39; rNSW=28; rank_mean=58.714; match_rank=53 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_8nt_mkv6_m3_shift0 (oligos_8nt_mkv6_m3)																		; oligos_8nt_mkv6_m3; m=0 (reference); ncol1=14; shift=0; ncol=15; wtATTGAGCAATaw- ; Alignment reference a 1041 669 2747 14 15 176 2352 4 72 3314 3314 89 1418 955 0 c 573 505 180 6 5 9 210 10 3149 10 9 291 657 749 0 g 791 682 325 9 20 3053 96 3305 6 4 4 213 534 676 0 t 930 1479 83 3306 3295 97 677 16 108 7 8 2742 726 955 0
MA0102.3_rc_shift1 (CEBPA_rc)		0.877	0.689	4.336	0.140	0.923	1.420	0.935	14	13	69	79	11	22	12	31.429	17	; oligos_8nt_mkv6_m3 versus MA0102.3_rc (CEBPA_rc); m=1/4; ncol2=11; w=11; offset=1; strand=R; shift=1; score=31.4286; -krTTrTGCAAt--- ; cor=0.877; Ncor=0.689; logoDP=4.336; NIcor=0.140; NsEucl=0.923; SSD=1.420; NSW=0.935; rcor=14; rNcor=13; rlogoDP=69; rNIcor=79; rNsEucl=11; rSSD=22; rNSW=12; rank_mean=31.429; match_rank=17 a 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 c 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 g 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 t 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0
MA0102.1_shift3 (Cebpa)		0.829	0.608	6.271	0.605	0.914	1.805	0.918	51	43	52	25	30	50	37	41.143	25	; oligos_8nt_mkv6_m3 versus MA0102.1 (Cebpa); m=2/4; ncol2=12; w=11; offset=3; strand=D; shift=3; score=41.1429; ---TtkygCAAyvyb ; cor=0.829; Ncor=0.608; logoDP=6.271; NIcor=0.605; NsEucl=0.914; SSD=1.805; NSW=0.918; rcor=51; rNcor=43; rlogoDP=52; rNIcor=25; rNsEucl=30; rSSD=50; rNSW=37; rank_mean=41.143; match_rank=25 a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
MA0466.1_rc_shift2 (CEBPB_rc)		0.872	0.685	2.615	-0.034	0.922	1.473	0.933	18	16	96	103	14	26	16	41.286	26	; oligos_8nt_mkv6_m3 versus MA0466.1_rc (CEBPB_rc); m=3/4; ncol2=11; w=11; offset=2; strand=R; shift=2; score=41.2857; --rTkrTGCAATm-- ; cor=0.872; Ncor=0.685; logoDP=2.615; NIcor=-0.034; NsEucl=0.922; SSD=1.473; NSW=0.933; rcor=18; rNcor=16; rlogoDP=96; rNIcor=103; rNsEucl=14; rSSD=26; rNSW=16; rank_mean=41.286; match_rank=26 a 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 c 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 g 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 t 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0
MA0102.2_shift3 (CEBPA)		0.843	0.542	6.270	0.533	0.898	1.680	0.907	38	72	53	39	74	37	51	52.000	45	; oligos_8nt_mkv6_m3 versus MA0102.2 (CEBPA); m=4/4; ncol2=9; w=9; offset=3; strand=D; shift=3; score= 52; ---TtkygCAAy--- ; cor=0.843; Ncor=0.542; logoDP=6.270; NIcor=0.533; NsEucl=0.898; SSD=1.680; NSW=0.907; rcor=38; rNcor=72; rlogoDP=53; rNIcor=39; rNsEucl=74; rSSD=37; rNSW=51; rank_mean=52.000; match_rank=45 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m1_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
dyads_m1_shift0 (dyads_m1)																		; dyads_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; wwTATtdhdhaATAww ; Alignment reference a 3310 3022 0 9626 0 1996 2451 2724 2823 3484 4759 9626 0 9626 3102 3127 c 1582 1807 0 0 0 1020 1192 2568 1511 2499 1851 0 0 0 1695 1607 g 1607 1695 0 0 0 1851 2499 1511 2568 1192 1020 0 0 0 1807 1582 t 3127 3102 9626 0 9626 4759 3484 2823 2724 2451 1996 0 9626 0 3022 3310
MA0033.1_shift6 (FOXL1)		0.924	0.462	4.378	0.472	0.947	0.357	0.978	5	99	68	53	1	1	1	32.571	19	; dyads_m1 versus MA0033.1 (FOXL1); m=1/2; ncol2=8; w=8; offset=6; strand=D; shift=6; score=32.5714; ------wwdayATA-- ; cor=0.924; Ncor=0.462; logoDP=4.378; NIcor=0.472; NsEucl=0.947; SSD=0.357; NSW=0.978; rcor=5; rNcor=99; rlogoDP=68; rNIcor=53; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=32.571; match_rank=19 a 0 0 0 0 0 0 7 10 6 13 4 21 0 22 0 0 c 0 0 0 0 0 0 1 4 3 4 10 0 2 1 0 0 g 0 0 0 0 0 0 4 2 6 4 2 2 0 0 0 0 t 0 0 0 0 0 0 11 7 8 2 7 0 21 0 0 0
MA0102.2_shift4 (CEBPA)		0.750	0.422	3.504	0.385	0.906	1.445	0.920	124	111	76	65	50	24	33	69.000	66	; dyads_m1 versus MA0102.2 (CEBPA); m=2/2; ncol2=9; w=9; offset=4; strand=D; shift=4; score= 69; ----TtkygCAAy--- ; cor=0.750; Ncor=0.422; logoDP=3.504; NIcor=0.385; NsEucl=0.906; SSD=1.445; NSW=0.920; rcor=124; rNcor=111; rlogoDP=76; rNIcor=65; rNsEucl=50; rSSD=24; rNSW=33; rank_mean=69.000; match_rank=66 a 0 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_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_m3_shift1 (oligos_7nt_mkv5_m3)																		; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=1; ncol=14; -wrTTACACAAya- ; Alignment reference a 0 701 1073 23 1 2580 0 2542 0 2578 2579 307 920 0 c 0 409 457 6 0 0 2580 0 2580 0 1 755 634 0 g 0 616 697 30 0 0 0 38 0 2 0 388 415 0 t 0 854 353 2521 2579 0 0 0 0 0 0 1130 611 0
MA0043.1_shift1 (HLF)		0.806	0.806	6.362	0.783	0.914	2.125	0.911	75	1	45	1	26	72	41	37.286	22	; oligos_7nt_mkv5_m3 versus MA0043.1 (HLF); m=1/8; ncol2=12; w=12; offset=0; strand=D; shift=1; score=37.2857; -krTTACryAAth- ; cor=0.806; Ncor=0.806; logoDP=6.362; NIcor=0.783; NsEucl=0.914; SSD=2.125; NSW=0.911; rcor=75; rNcor=1; rlogoDP=45; rNIcor=1; rNsEucl=26; rSSD=72; rNSW=41; rank_mean=37.286; match_rank=22 a 0 1 6 1 0 13 0 6 0 13 15 2 5 0 c 0 4 0 0 0 1 15 0 9 4 0 3 5 0 g 0 8 12 0 3 2 1 12 0 1 1 1 3 0 t 0 5 0 17 15 2 2 0 9 0 2 12 5 0
MA0102.3_shift2 (CEBPA)		0.806	0.738	9.392	0.733	0.905	2.166	0.902	76	4	24	3	52	77	59	42.143	28	; oligos_7nt_mkv5_m3 versus MA0102.3 (CEBPA); m=2/8; ncol2=11; w=11; offset=1; strand=D; shift=2; score=42.1429; --aTTGCAyAAym- ; cor=0.806; Ncor=0.738; logoDP=9.392; NIcor=0.733; NsEucl=0.905; SSD=2.166; NSW=0.902; rcor=76; rNcor=4; rlogoDP=24; rNIcor=3; rNsEucl=52; rSSD=77; rNSW=59; rank_mean=42.143; match_rank=28 a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0466.1_shift1 (CEBPB)		0.769	0.705	9.034	0.691	0.897	2.567	0.883	106	9	30	9	76	109	93	61.714	58	; oligos_7nt_mkv5_m3 versus MA0466.1 (CEBPB); m=3/8; ncol2=11; w=11; offset=0; strand=D; shift=1; score=61.7143; -kATTGCAymAy-- ; cor=0.769; Ncor=0.705; logoDP=9.034; NIcor=0.691; NsEucl=0.897; SSD=2.567; NSW=0.883; rcor=106; rNcor=9; rlogoDP=30; rNIcor=9; rNsEucl=76; rSSD=109; rNSW=93; rank_mean=61.714; match_rank=58 a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0442.1_rc_shift7 (SOX10_rc)		0.842	0.421	0.061	-0.129	0.885	0.948	0.921	39	112	124	111	107	7	30	75.714	80	; oligos_7nt_mkv5_m3 versus MA0442.1_rc (SOX10_rc); m=4/8; ncol2=6; w=6; offset=6; strand=R; shift=7; score=75.7143; -------ACAAwG- ; cor=0.842; Ncor=0.421; logoDP=0.061; NIcor=-0.129; NsEucl=0.885; SSD=0.948; NSW=0.921; rcor=39; rNcor=112; rlogoDP=124; rNIcor=111; rNsEucl=107; rSSD=7; rNSW=30; rank_mean=75.714; match_rank=80 a 0 0 0 0 0 0 0 21 0 22 17 10 3 0 c 0 0 0 0 0 0 0 1 19 0 4 2 0 0 g 0 0 0 0 0 0 0 0 3 0 1 2 19 0 t 0 0 0 0 0 0 0 0 0 0 0 8 0 0
MA0102.2_shift3 (CEBPA)		0.775	0.581	6.445	0.550	0.878	2.408	0.866	99	52	44	34	116	98	119	80.286	90	; oligos_7nt_mkv5_m3 versus MA0102.2 (CEBPA); m=5/8; ncol2=9; w=9; offset=2; strand=D; shift=3; score=80.2857; ---TtkygCAAy-- ; cor=0.775; Ncor=0.581; logoDP=6.445; NIcor=0.550; NsEucl=0.878; SSD=2.408; NSW=0.866; rcor=99; rNcor=52; rlogoDP=44; rNIcor=34; rNsEucl=116; rSSD=98; rNSW=119; rank_mean=80.286; match_rank=90 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0
MA0102.1_shift3 (Cebpa)		0.770	0.550	6.445	0.526	0.889	2.451	0.877	104	68	43	41	100	102	105	80.429	91	; oligos_7nt_mkv5_m3 versus MA0102.1 (Cebpa); m=6/8; ncol2=12; w=10; offset=2; strand=D; shift=3; score=80.4286; ---TtkygCAAyvy ; cor=0.770; Ncor=0.550; logoDP=6.445; NIcor=0.526; NsEucl=0.889; SSD=2.451; NSW=0.877; rcor=104; rNcor=68; rlogoDP=43; rNIcor=41; rNsEucl=100; rSSD=102; rNSW=105; rank_mean=80.429; match_rank=91 a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 t 0 0 0 15 12 7 5 2 1 0 0 10 2 8
MA0025.1_rc_shift0 (NFIL3_rc)		0.798	0.614	2.419	0.080	0.893	2.274	0.886	81	40	100	88	89	86	91	82.143	93	; oligos_7nt_mkv5_m3 versus MA0025.1_rc (NFIL3_rc); m=7/8; ncol2=11; w=10; offset=-1; strand=R; shift=0; score=82.1429; ayrTTACrTAA--- ; cor=0.798; Ncor=0.614; logoDP=2.419; NIcor=0.080; NsEucl=0.893; SSD=2.274; NSW=0.886; rcor=81; rNcor=40; rlogoDP=100; rNIcor=88; rNsEucl=89; rSSD=86; rNSW=91; rank_mean=82.143; match_rank=93 a 10 4 8 0 0 23 0 15 1 21 22 0 0 0 c 3 7 4 1 0 0 21 0 0 2 0 0 0 0 g 5 5 11 0 0 0 0 8 0 0 0 0 0 0 t 5 7 0 22 23 0 2 0 22 0 1 0 0 0
MA0078.1_rc_shift6 (Sox17_rc)		0.814	0.407	2.071	0.097	0.879	1.427	0.898	63	119	105	86	114	23	68	82.571	95	; oligos_7nt_mkv5_m3 versus MA0078.1_rc (Sox17_rc); m=8/8; ncol2=9; w=7; offset=5; strand=R; shift=6; score=82.5714; ------sACAATrd ; cor=0.814; Ncor=0.407; logoDP=2.071; NIcor=0.097; NsEucl=0.879; SSD=1.427; NSW=0.898; rcor=63; rNcor=119; rlogoDP=105; rNIcor=86; rNsEucl=114; rSSD=23; rNSW=68; rank_mean=82.571; match_rank=95 a 0 0 0 0 0 0 4 29 0 31 30 1 9 11 c 0 0 0 0 0 0 10 2 31 0 0 0 1 4 g 0 0 0 0 0 0 17 0 0 0 1 0 18 8 t 0 0 0 0 0 0 0 0 0 0 0 30 3 8

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m3_shift0 (positions_7nt_m3)																		; positions_7nt_m3; m=0 (reference); ncol1=16; shift=0; ncol=16; arAGATTGCGAAATrw ; Alignment reference a 162 113 401 15 413 0 0 7 36 40 396 423 432 2 126 150 c 77 108 4 27 6 0 0 0 303 14 17 10 0 15 102 90 g 98 128 9 350 11 0 1 422 24 365 2 0 1 7 112 76 t 96 84 19 41 3 433 432 4 70 14 18 0 0 409 93 117
MA0102.2_rc_shift4 (CEBPA_rc)		0.914	0.514	3.780	0.178	0.918	1.082	0.940	7	83	75	73	18	10	9	39.286	24	; positions_7nt_m3 versus MA0102.2_rc (CEBPA_rc); m=1/4; ncol2=9; w=9; offset=4; strand=R; shift=4; score=39.2857; ----rTTGcrmaA--- ; cor=0.914; Ncor=0.514; logoDP=3.780; NIcor=0.178; NsEucl=0.918; SSD=1.082; NSW=0.940; rcor=7; rNcor=83; rlogoDP=75; rNIcor=73; rNsEucl=18; rSSD=10; rNSW=9; rank_mean=39.286; match_rank=24 a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.1_rc_shift1 (Cebpa_rc)		0.876	0.657	0.379	-0.211	0.922	1.748	0.927	15	22	112	123	13	42	22	49.857	41	; positions_7nt_m3 versus MA0102.1_rc (Cebpa_rc); m=2/4; ncol2=12; w=12; offset=1; strand=R; shift=1; score=49.8571; -vrbrTTGcrmaA--- ; cor=0.876; Ncor=0.657; logoDP=0.379; NIcor=-0.211; NsEucl=0.922; SSD=1.748; NSW=0.927; rcor=15; rNcor=22; rlogoDP=112; rNIcor=123; rNsEucl=13; rSSD=42; rNSW=22; rank_mean=49.857; match_rank=41 a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.3_shift4 (CEBPA)		0.763	0.524	8.483	0.503	0.894	2.703	0.877	109	80	34	45	86	116	106	82.286	94	; positions_7nt_m3 versus MA0102.3 (CEBPA); m=3/4; ncol2=11; w=11; offset=4; strand=D; shift=4; score=82.2857; ----aTTGCAyAAym- ; cor=0.763; Ncor=0.524; logoDP=8.483; NIcor=0.503; NsEucl=0.894; SSD=2.703; NSW=0.877; rcor=109; rNcor=80; rlogoDP=34; rNIcor=45; rNsEucl=86; rSSD=116; rNSW=106; rank_mean=82.286; match_rank=94 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0466.1_rc_shift4 (CEBPB_rc)		0.756	0.520	3.051	0.047	0.893	2.788	0.873	118	81	84	96	91	118	110	99.714	120	; positions_7nt_m3 versus MA0466.1_rc (CEBPB_rc); m=4/4; ncol2=11; w=11; offset=4; strand=R; shift=4; score=99.7143; ----rTkrTGCAATm- ; cor=0.756; Ncor=0.520; logoDP=3.051; NIcor=0.047; NsEucl=0.893; SSD=2.788; NSW=0.873; rcor=118; rNcor=81; rlogoDP=84; rNIcor=96; rNsEucl=91; rSSD=118; rNSW=110; rank_mean=99.714; match_rank=120 a 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m5_shift2 (oligos_7nt_mkv5_m5)																		; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --wrTTGCTCAAya ; Alignment reference a 0 0 790 1154 0 0 0 0 5 0 2774 2774 284 977 c 0 0 474 551 0 1 0 2774 0 2774 0 0 848 665 g 0 0 595 751 0 0 2774 0 6 0 0 0 483 459 t 0 0 915 318 2774 2773 0 0 2763 0 0 0 1159 673
MA0102.3_shift3 (CEBPA)		0.803	0.736	9.718	0.722	0.904	2.208	0.900	78	5	14	5	53	81	63	42.714	30	; oligos_7nt_mkv5_m5 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=1; strand=D; shift=3; score=42.7143; ---aTTGCAyAAym ; cor=0.803; Ncor=0.736; logoDP=9.718; NIcor=0.722; NsEucl=0.904; SSD=2.208; NSW=0.900; rcor=78; rNcor=5; rlogoDP=14; rNIcor=5; rNsEucl=53; rSSD=81; rNSW=63; rank_mean=42.714; match_rank=30 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661
MA0466.1_shift2 (CEBPB)		0.780	0.715	9.502	0.692	0.899	2.475	0.888	93	8	21	8	72	103	89	56.286	50	; oligos_7nt_mkv5_m5 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=0; strand=D; shift=2; score=56.2857; --kATTGCAymAy- ; cor=0.780; Ncor=0.715; logoDP=9.502; NIcor=0.692; NsEucl=0.899; SSD=2.475; NSW=0.888; rcor=93; rNcor=8; rlogoDP=21; rNIcor=8; rNsEucl=72; rSSD=103; rNSW=89; rank_mean=56.286; match_rank=50 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0
MA0102.2_rc_shift3 (CEBPA_rc)		0.784	0.588	2.577	0.065	0.880	2.349	0.870	87	50	98	90	113	92	116	92.286	112	; oligos_7nt_mkv5_m5 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=1; strand=R; shift=3; score=92.2857; ---rTTGcrmaA-- ; cor=0.784; Ncor=0.588; logoDP=2.577; NIcor=0.065; NsEucl=0.880; SSD=2.349; NSW=0.870; rcor=87; rNcor=50; rlogoDP=98; rNIcor=90; rNsEucl=113; rSSD=92; rNSW=116; rank_mean=92.286; match_rank=112 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0
MA0102.1_rc_shift0 (Cebpa_rc)		0.778	0.556	0.504	-0.105	0.890	2.407	0.880	97	65	110	110	96	97	101	96.571	115	; oligos_7nt_mkv5_m5 versus MA0102.1_rc (Cebpa_rc); m=4/4; ncol2=12; w=10; offset=-2; strand=R; shift=0; score=96.5714; vrbrTTGcrmaA-- ; cor=0.778; Ncor=0.556; logoDP=0.504; NIcor=-0.105; NsEucl=0.890; SSD=2.407; NSW=0.880; rcor=97; rNcor=65; rlogoDP=110; rNIcor=110; rNsEucl=96; rSSD=97; rNSW=101; rank_mean=96.571; match_rank=115 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_8nt_mkv6_m5_shift2 (oligos_8nt_mkv6_m5)																		; oligos_8nt_mkv6_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --waTTGCCCAAya ; Alignment reference a 0 0 519 683 0 0 0 0 5 0 1878 1880 230 606 c 0 0 405 470 0 0 0 1881 1825 1880 0 1 573 394 g 0 0 401 453 0 0 1879 0 50 0 3 0 432 449 t 0 0 556 275 1881 1881 2 0 1 1 0 0 646 432
MA0102.3_shift3 (CEBPA)		0.797	0.731	9.686	0.721	0.904	2.236	0.898	83	6	16	6	55	83	67	45.143	34	; oligos_8nt_mkv6_m5 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=1; strand=D; shift=3; score=45.1429; ---aTTGCAyAAym ; cor=0.797; Ncor=0.731; logoDP=9.686; NIcor=0.721; NsEucl=0.904; SSD=2.236; NSW=0.898; rcor=83; rNcor=6; rlogoDP=16; rNIcor=6; rNsEucl=55; rSSD=83; rNSW=67; rank_mean=45.143; match_rank=34 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661
MA0466.1_shift2 (CEBPB)		0.762	0.698	9.425	0.689	0.896	2.628	0.881	110	10	23	10	78	113	100	63.429	59	; oligos_8nt_mkv6_m5 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=0; strand=D; shift=2; score=63.4286; --kATTGCAymAy- ; cor=0.762; Ncor=0.698; logoDP=9.425; NIcor=0.689; NsEucl=0.896; SSD=2.628; NSW=0.881; rcor=110; rNcor=10; rlogoDP=23; rNIcor=10; rNsEucl=78; rSSD=113; rNSW=100; rank_mean=63.429; match_rank=59 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0
MA0102.2_rc_shift3 (CEBPA_rc)		0.783	0.588	3.321	0.198	0.880	2.319	0.871	89	51	77	71	112	89	114	86.143	103	; oligos_8nt_mkv6_m5 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=1; strand=R; shift=3; score=86.1429; ---rTTGcrmaA-- ; cor=0.783; Ncor=0.588; logoDP=3.321; NIcor=0.198; NsEucl=0.880; SSD=2.319; NSW=0.871; rcor=89; rNcor=51; rlogoDP=77; rNIcor=71; rNsEucl=112; rSSD=89; rNSW=114; rank_mean=86.143; match_rank=103 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0
MA0102.1_rc_shift0 (Cebpa_rc)		0.778	0.556	0.345	-0.146	0.891	2.364	0.882	96	64	116	113	95	93	98	96.429	114	; oligos_8nt_mkv6_m5 versus MA0102.1_rc (Cebpa_rc); m=4/4; ncol2=12; w=10; offset=-2; strand=R; shift=0; score=96.4286; vrbrTTGcrmaA-- ; cor=0.778; Ncor=0.556; logoDP=0.345; NIcor=-0.146; NsEucl=0.891; SSD=2.364; NSW=0.882; rcor=96; rNcor=64; rlogoDP=116; rNIcor=113; rNsEucl=95; rSSD=93; rNSW=98; rank_mean=96.429; match_rank=114 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0

One-to-n matrix alignment; reference matrix: positions_8nt_m2_shift1 ; 7 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_8nt_m2_shift1 (positions_8nt_m2)																		; positions_8nt_m2; m=0 (reference); ncol1=16; shift=1; ncol=17; -wrTGATTGTGCAAgad ; Alignment reference a 0 183 173 43 19 589 4 1 23 18 1 24 634 632 19 271 166 c 0 144 131 13 20 12 4 1 4 12 1 586 4 0 72 129 147 g 0 140 178 24 576 24 1 10 594 7 632 3 0 4 406 107 165 t 0 171 156 558 23 13 629 626 17 601 4 25 0 2 141 131 160
MA0466.1_rc_shift5 (CEBPB_rc)		0.871	0.599	2.668	-0.037	0.920	1.536	0.930	20	47	92	104	15	28	18	46.286	35	; positions_8nt_m2 versus MA0466.1_rc (CEBPB_rc); m=1/6; ncol2=11; w=11; offset=4; strand=R; shift=5; score=46.2857; -----rTkrTGCAATm- ; cor=0.871; Ncor=0.599; logoDP=2.668; NIcor=-0.037; NsEucl=0.920; SSD=1.536; NSW=0.930; rcor=20; rNcor=47; rlogoDP=92; rNIcor=104; rNsEucl=15; rSSD=28; rNSW=18; rank_mean=46.286; match_rank=35 a 0 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 c 0 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 g 0 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 t 0 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0
MA0102.3_rc_shift4 (CEBPA_rc)		0.862	0.593	4.265	0.040	0.914	1.774	0.919	22	49	70	98	25	46	34	49.143	40	; positions_8nt_m2 versus MA0102.3_rc (CEBPA_rc); m=2/6; ncol2=11; w=11; offset=3; strand=R; shift=4; score=49.1429; ----krTTrTGCAAt-- ; cor=0.862; Ncor=0.593; logoDP=4.265; NIcor=0.040; NsEucl=0.914; SSD=1.774; NSW=0.919; rcor=22; rNcor=49; rlogoDP=70; rNIcor=98; rNsEucl=25; rSSD=46; rNSW=34; rank_mean=49.143; match_rank=40 a 0 0 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 c 0 0 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 g 0 0 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 t 0 0 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0
MA0102.1_shift6 (Cebpa)		0.780	0.505	6.062	0.491	0.904	2.253	0.898	92	87	63	47	56	85	71	71.571	72	; positions_8nt_m2 versus MA0102.1 (Cebpa); m=3/6; ncol2=12; w=11; offset=5; strand=D; shift=6; score=71.5714; ------TtkygCAAyvy ; cor=0.780; Ncor=0.505; logoDP=6.062; NIcor=0.491; NsEucl=0.904; SSD=2.253; NSW=0.898; rcor=92; rNcor=87; rlogoDP=63; rNIcor=47; rNsEucl=56; rSSD=85; rNSW=71; rank_mean=71.571; match_rank=72 a 0 0 0 0 0 0 3 1 4 2 4 2 18 18 0 5 2 c 0 0 0 0 0 0 0 1 1 9 2 15 0 0 6 6 5 g 0 0 0 0 0 0 0 4 6 2 10 0 0 0 2 5 3 t 0 0 0 0 0 0 15 12 7 5 2 1 0 0 10 2 8
MA0038.1_rc_shift0 (Gfi1_rc)		0.779	0.413	0.367	-0.139	0.895	1.770	0.902	94	116	113	112	81	44	58	88.286	107	; positions_8nt_m2 versus MA0038.1_rc (Gfi1_rc); m=4/6; ncol2=10; w=9; offset=-1; strand=R; shift=0; score=88.2857; cwgtGATTkr------- ; cor=0.779; Ncor=0.413; logoDP=0.367; NIcor=-0.139; NsEucl=0.895; SSD=1.770; NSW=0.902; rcor=94; rNcor=116; rlogoDP=113; rNIcor=112; rNsEucl=81; rSSD=44; rNSW=58; rank_mean=88.286; match_rank=107 a 5 21 6 13 0 51 0 0 2 15 0 0 0 0 0 0 0 c 28 2 11 2 0 1 0 0 7 9 0 0 0 0 0 0 0 g 13 11 28 7 52 0 0 0 16 20 0 0 0 0 0 0 0 t 7 19 8 31 1 1 53 53 28 9 0 0 0 0 0 0 0
MA0102.2_rc_shift5 (CEBPA_rc)		0.812	0.457	2.608	0.048	0.885	2.126	0.882	66	100	97	94	106	73	97	90.429	110	; positions_8nt_m2 versus MA0102.2_rc (CEBPA_rc); m=5/6; ncol2=9; w=9; offset=4; strand=R; shift=5; score=90.4286; -----rTTGcrmaA--- ; cor=0.812; Ncor=0.457; logoDP=2.608; NIcor=0.048; NsEucl=0.885; SSD=2.126; NSW=0.882; rcor=66; rNcor=100; rlogoDP=97; rNIcor=94; rNsEucl=106; rSSD=73; rNSW=97; rank_mean=90.429; match_rank=110 a 0 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0078.1_shift2 (Sox17)		0.752	0.423	7.158	0.424	0.881	2.296	0.872	121	110	38	60	110	88	112	91.286	111	; positions_8nt_m2 versus MA0078.1 (Sox17); m=6/6; ncol2=9; w=9; offset=1; strand=D; shift=2; score=91.2857; --yhyATTGTs------ ; cor=0.752; Ncor=0.423; logoDP=7.158; NIcor=0.424; NsEucl=0.881; SSD=2.296; NSW=0.872; rcor=121; rNcor=110; rlogoDP=38; rNIcor=60; rNsEucl=110; rSSD=88; rNSW=112; rank_mean=91.286; match_rank=111 a 0 0 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 c 0 0 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 g 0 0 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 t 0 0 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m3_shift0 (dyads_m3)																		; dyads_m3; m=0 (reference); ncol1=10; shift=0; ncol=12; wdTTGCAAhw-- ; Alignment reference a 3278 3895 0 0 0 0 12984 12984 4097 5695 0 0 c 1633 1516 0 0 0 12984 0 0 3476 2378 0 0 g 2378 3476 0 0 12984 0 0 0 1516 1633 0 0 t 5695 4097 12984 12984 0 0 0 0 3895 3278 0 0
MA0019.1_shift0 (Ddit3::Cebpa)		0.778	0.648	7.559	0.663	0.902	1.936	0.903	98	28	35	13	62	59	55	50.000	42	; dyads_m3 versus MA0019.1 (Ddit3::Cebpa); m=1/3; ncol2=12; w=10; offset=0; strand=D; shift=0; score= 50; rrrTGCAATmcc ; cor=0.778; Ncor=0.648; logoDP=7.559; NIcor=0.663; NsEucl=0.902; SSD=1.936; NSW=0.903; rcor=98; rNcor=28; rlogoDP=35; rNIcor=13; rNsEucl=62; rSSD=59; rNSW=55; rank_mean=50.000; match_rank=42 a 14 11 18 0 0 4 38 36 0 14 4 0 c 7 7 3 1 0 33 1 2 6 17 23 26 g 12 14 15 0 38 0 0 1 0 5 9 6 t 6 7 3 38 1 2 0 0 33 3 3 7
MA0133.1_shift4 (BRCA1)		0.779	0.425	3.282	0.420	0.870	1.212	0.899	95	108	78	61	120	16	64	77.429	85	; dyads_m3 versus MA0133.1 (BRCA1); m=2/3; ncol2=7; w=6; offset=4; strand=D; shift=4; score=77.4286; ----mCAAcms- ; cor=0.779; Ncor=0.425; logoDP=3.282; NIcor=0.420; NsEucl=0.870; SSD=1.212; NSW=0.899; rcor=95; rNcor=108; rlogoDP=78; rNIcor=61; rNsEucl=120; rSSD=16; rNSW=64; rank_mean=77.429; match_rank=85 a 0 0 0 0 15 4 41 36 7 19 3 0 c 0 0 0 0 11 35 1 2 29 14 22 0 g 0 0 0 0 10 2 1 4 6 7 15 0 t 0 0 0 0 7 2 0 1 1 3 3 0
MA0102.3_shift1 (CEBPA)		0.756	0.567	7.319	0.532	0.883	2.233	0.876	117	60	37	40	109	82	107	78.857	88	; dyads_m3 versus MA0102.3 (CEBPA); m=3/3; ncol2=11; w=9; offset=1; strand=D; shift=1; score=78.8571; -aTTGCAyAAym ; cor=0.756; Ncor=0.567; logoDP=7.319; NIcor=0.532; NsEucl=0.883; SSD=2.233; NSW=0.876; rcor=117; rNcor=60; rlogoDP=37; rNIcor=40; rNsEucl=109; rSSD=82; rNSW=107; rank_mean=78.857; match_rank=88 a 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 c 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 g 0 3635 0 0 11304 0 1066 0 0 0 1804 890 t 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)																		; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; wwAGATTGTGAAAtm ; Alignment reference a 357 259 768 43 865 5 8 36 26 3 721 847 870 59 359 c 127 176 19 23 8 5 2 2 40 1 79 31 2 182 239 g 172 215 31 695 16 3 17 850 7 885 6 5 14 114 107 t 237 243 75 132 4 880 866 5 820 4 87 10 7 538 188
MA0102.3_rc_shift3 (CEBPA_rc)		0.845	0.619	4.056	0.122	0.913	1.840	0.916	35	37	74	82	32	54	39	50.429	43	; positions_6nt_m1 versus MA0102.3_rc (CEBPA_rc); m=1/5; ncol2=11; w=11; offset=3; strand=R; shift=3; score=50.4286; ---krTTrTGCAAt- ; cor=0.845; Ncor=0.619; logoDP=4.056; NIcor=0.122; NsEucl=0.913; SSD=1.840; NSW=0.916; rcor=35; rNcor=37; rlogoDP=74; rNIcor=82; rNsEucl=32; rSSD=54; rNSW=39; rank_mean=50.429; match_rank=43 a 0 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 c 0 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 g 0 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 t 0 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0
MA0466.1_rc_shift4 (CEBPB_rc)		0.845	0.620	2.705	0.034	0.915	1.747	0.921	34	36	91	100	24	41	31	51.000	44	; positions_6nt_m1 versus MA0466.1_rc (CEBPB_rc); m=2/5; ncol2=11; w=11; offset=4; strand=R; shift=4; score= 51; ----rTkrTGCAATm ; cor=0.845; Ncor=0.620; logoDP=2.705; NIcor=0.034; NsEucl=0.915; SSD=1.747; NSW=0.921; rcor=34; rNcor=36; rlogoDP=91; rNIcor=100; rNsEucl=24; rSSD=41; rNSW=31; rank_mean=51.000; match_rank=44 a 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006
MA0102.2_rc_shift4 (CEBPA_rc)		0.835	0.501	3.041	0.152	0.894	1.828	0.898	46	90	85	76	87	52	66	71.714	73	; positions_6nt_m1 versus MA0102.2_rc (CEBPA_rc); m=3/5; ncol2=9; w=9; offset=4; strand=R; shift=4; score=71.7143; ----rTTGcrmaA-- ; cor=0.835; Ncor=0.501; logoDP=3.041; NIcor=0.152; NsEucl=0.894; SSD=1.828; NSW=0.898; rcor=46; rNcor=90; rlogoDP=85; rNIcor=76; rNsEucl=87; rSSD=52; rNSW=66; rank_mean=71.714; match_rank=73 a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0
MA0102.1_rc_shift1 (Cebpa_rc)		0.807	0.646	0.416	-0.221	0.908	2.428	0.899	74	29	111	124	39	100	65	77.429	84	; positions_6nt_m1 versus MA0102.1_rc (Cebpa_rc); m=4/5; ncol2=12; w=12; offset=1; strand=R; shift=1; score=77.4286; -vrbrTTGcrmaA-- ; cor=0.807; Ncor=0.646; logoDP=0.416; NIcor=-0.221; NsEucl=0.908; SSD=2.428; NSW=0.899; rcor=74; rNcor=29; rlogoDP=111; rNIcor=124; rNsEucl=39; rSSD=100; rNSW=65; rank_mean=77.429; match_rank=84 a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0
MA0078.1_shift1 (Sox17)		0.760	0.456	7.372	0.461	0.884	2.179	0.879	114	101	36	55	108	78	102	84.857	100	; positions_6nt_m1 versus MA0078.1 (Sox17); m=5/5; ncol2=9; w=9; offset=1; strand=D; shift=1; score=84.8571; -yhyATTGTs----- ; cor=0.760; Ncor=0.456; logoDP=7.372; NIcor=0.461; NsEucl=0.884; SSD=2.179; NSW=0.879; rcor=114; rNcor=101; rlogoDP=36; rNIcor=55; rNsEucl=108; rSSD=78; rNSW=102; rank_mean=84.857; match_rank=100 a 0 7 8 3 30 0 0 0 0 0 0 0 0 0 0 c 0 9 8 18 0 1 0 0 0 17 0 0 0 0 0 g 0 6 4 1 0 0 0 31 2 10 0 0 0 0 0 t 0 9 11 9 1 30 31 0 29 4 0 0 0 0 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m4_shift2 (oligos_7nt_mkv5_m4)																		; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --aaACAAAAACaa ; Alignment reference a 0 0 596 606 1117 0 1138 1144 1145 1145 1145 0 621 489 c 0 0 148 179 6 1145 0 0 0 0 0 1145 225 198 g 0 0 165 156 9 0 7 0 0 0 0 0 78 212 t 0 0 236 204 13 0 0 1 0 0 0 0 221 246
MA0084.1_shift0 (SRY)		0.847	0.424	6.343	0.414	0.893	1.115	0.920	33	109	46	62	90	12	32	54.857	47	; oligos_7nt_mkv5_m4 versus MA0084.1 (SRY); m=1/1; ncol2=9; w=7; offset=-2; strand=D; shift=0; score=54.8571; kwwaACAAw----- ; cor=0.847; Ncor=0.424; logoDP=6.343; NIcor=0.414; NsEucl=0.893; SSD=1.115; NSW=0.920; rcor=33; rNcor=109; rlogoDP=46; rNIcor=62; rNsEucl=90; rSSD=12; rNSW=32; rank_mean=54.857; match_rank=47 a 5 8 15 18 25 0 28 27 7 0 0 0 0 0 c 5 3 0 3 0 26 0 0 0 0 0 0 0 0 g 10 4 3 3 0 0 0 1 2 0 0 0 0 0 t 8 13 10 4 3 2 0 0 19 0 0 0 0 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)																		; positions_6nt_m4; m=0 (reference); ncol1=18; shift=0; ncol=18; wsATGTTGCACAACAGtr ; Alignment reference a 39 29 88 5 6 0 1 4 2 115 3 118 117 2 106 5 21 32 c 22 32 16 1 4 0 0 0 114 0 110 0 0 110 2 8 25 29 g 27 31 7 0 106 0 0 110 1 0 1 0 0 3 2 99 25 33 t 30 26 7 112 2 118 117 4 1 3 4 0 1 3 8 6 47 24
MA0102.3_shift4 (CEBPA)		0.830	0.507	9.852	0.484	0.903	2.285	0.896	49	85	9	50	58	87	73	58.714	52	; positions_6nt_m4 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=4; strand=D; shift=4; score=58.7143; ----aTTGCAyAAym--- ; cor=0.830; Ncor=0.507; logoDP=9.852; NIcor=0.484; NsEucl=0.903; SSD=2.285; NSW=0.896; rcor=49; rNcor=85; rlogoDP=9; rNIcor=50; rNsEucl=58; rSSD=87; rNSW=73; rank_mean=58.714; match_rank=52 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0 0
MA0466.1_shift3 (CEBPB)		0.788	0.482	9.597	0.452	0.892	2.819	0.872	85	96	19	56	93	120	113	83.143	97	; positions_6nt_m4 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score=83.1429; ---kATTGCAymAy---- ; cor=0.788; Ncor=0.482; logoDP=9.597; NIcor=0.452; NsEucl=0.892; SSD=2.819; NSW=0.872; rcor=85; rNcor=96; rlogoDP=19; rNIcor=56; rNsEucl=93; rSSD=120; rNSW=113; rank_mean=83.143; match_rank=97 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0 0
MA0102.1_rc_shift1 (Cebpa_rc)		0.751	0.500	0.359	-0.161	0.895	3.152	0.869	123	91	114	116	83	124	118	109.857	123	; positions_6nt_m4 versus MA0102.1_rc (Cebpa_rc); m=3/3; ncol2=12; w=12; offset=1; strand=R; shift=1; score=109.857; -vrbrTTGcrmaA----- ; cor=0.751; Ncor=0.500; logoDP=0.359; NIcor=-0.161; NsEucl=0.895; SSD=3.152; NSW=0.869; rcor=123; rNcor=91; rlogoDP=114; rNIcor=116; rNsEucl=83; rSSD=124; rNSW=118; rank_mean=109.857; match_rank=123 a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 0 0 c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 0 0 g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 0 0 t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0 0 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)																		; positions_6nt_m2; m=0 (reference); ncol1=15; shift=0; ncol=15; dkATTACGCAAGArw ; Alignment reference a 201 156 603 2 1 580 30 65 11 668 668 9 620 178 200 c 107 113 23 2 2 3 534 20 638 1 0 57 15 145 138 g 172 198 33 1 11 48 28 569 1 0 1 531 14 185 143 t 189 202 10 664 655 38 77 15 19 0 0 72 20 161 188
MA0102.2_shift3 (CEBPA)		0.819	0.492	6.241	0.485	0.895	1.789	0.901	59	93	55	49	84	47	61	64.000	60	; positions_6nt_m2 versus MA0102.2 (CEBPA); m=1/2; ncol2=9; w=9; offset=3; strand=D; shift=3; score= 64; ---TtkygCAAy--- ; cor=0.819; Ncor=0.492; logoDP=6.241; NIcor=0.485; NsEucl=0.895; SSD=1.789; NSW=0.901; rcor=59; rNcor=93; rlogoDP=55; rNIcor=49; rNsEucl=84; rSSD=47; rNSW=61; rank_mean=64.000; match_rank=60 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
MA0102.1_shift3 (Cebpa)		0.760	0.608	6.260	0.606	0.906	2.543	0.894	113	42	54	24	47	106	75	65.857	65	; positions_6nt_m2 versus MA0102.1 (Cebpa); m=2/2; ncol2=12; w=12; offset=3; strand=D; shift=3; score=65.8571; ---TtkygCAAyvyb ; cor=0.760; Ncor=0.608; logoDP=6.260; NIcor=0.606; NsEucl=0.906; SSD=2.543; NSW=0.894; rcor=113; rNcor=42; rlogoDP=54; rNIcor=24; rNsEucl=47; rSSD=106; rNSW=75; rank_mean=65.857; match_rank=65 a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m4_shift0 (positions_7nt_m4)																		; positions_7nt_m4; m=0 (reference); ncol1=17; shift=0; ncol=17; wyCTCTTGCACAACTbh ; Alignment reference a 53 47 13 1 20 0 1 2 0 180 11 195 197 3 6 36 50 c 42 60 160 8 160 0 0 0 198 8 185 2 1 178 15 53 54 g 45 38 9 0 18 0 1 189 1 3 1 1 0 3 3 54 24 t 59 54 17 190 1 199 197 8 0 8 2 1 1 15 175 56 71
MA0102.3_shift4 (CEBPA)		0.811	0.525	9.742	0.510	0.900	2.404	0.891	70	79	13	44	67	96	82	64.429	61	; positions_7nt_m4 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=4; strand=D; shift=4; score=64.4286; ----aTTGCAyAAym-- ; cor=0.811; Ncor=0.525; logoDP=9.742; NIcor=0.510; NsEucl=0.900; SSD=2.404; NSW=0.891; rcor=70; rNcor=79; rlogoDP=13; rNIcor=44; rNsEucl=67; rSSD=96; rNSW=82; rank_mean=64.429; match_rank=61 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0466.1_shift3 (CEBPB)		0.791	0.512	9.574	0.490	0.895	2.676	0.878	84	84	20	48	85	115	103	77.000	83	; positions_7nt_m4 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 77; ---kATTGCAymAy--- ; cor=0.791; Ncor=0.512; logoDP=9.574; NIcor=0.490; NsEucl=0.895; SSD=2.676; NSW=0.878; rcor=84; rNcor=84; rlogoDP=20; rNIcor=48; rNsEucl=85; rSSD=115; rNSW=103; rank_mean=77.000; match_rank=83 a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0102.2_shift5 (CEBPA)		0.774	0.410	6.117	0.384	0.877	2.446	0.864	100	118	60	66	117	101	120	97.429	117	; positions_7nt_m4 versus MA0102.2 (CEBPA); m=3/3; ncol2=9; w=9; offset=5; strand=D; shift=5; score=97.4286; -----TtkygCAAy--- ; cor=0.774; Ncor=0.410; logoDP=6.117; NIcor=0.384; NsEucl=0.877; SSD=2.446; NSW=0.864; rcor=100; rNcor=118; rlogoDP=60; rNIcor=66; rNsEucl=117; rSSD=101; rNSW=120; rank_mean=97.429; match_rank=117 a 0 0 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)																		; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=13; shift=0; ncol=14; ttTTCTTTTCTtt- ; Alignment reference a 284 285 145 199 3 0 6 8 4 1 7 298 281 0 c 250 209 51 47 1336 0 0 0 1 1338 14 258 292 0 g 215 182 43 30 0 11 1 0 0 0 46 236 177 0 t 590 663 1100 1063 0 1328 1332 1331 1334 0 1272 547 589 0
MA0035.3_shift2 (Gata1)		0.767	0.649	9.313	0.658	0.896	2.612	0.881	107	26	26	14	77	111	99	65.714	64	; oligos_6nt_mkv4_m4 versus MA0035.3 (Gata1); m=1/3; ncol2=11; w=11; offset=2; strand=D; shift=2; score=65.7143; --tyCTTATCTsy- ; cor=0.767; Ncor=0.649; logoDP=9.313; NIcor=0.658; NsEucl=0.896; SSD=2.612; NSW=0.881; rcor=107; rNcor=26; rlogoDP=26; rNIcor=14; rNsEucl=77; rSSD=111; rNSW=99; rank_mean=65.714; match_rank=64 a 0 0 2035 506 0 0 0 17955 0 0 2166 2502 1886 0 c 0 0 4321 6406 14869 697 0 0 0 17955 0 6166 5072 0 g 0 0 2530 2792 437 0 0 0 0 0 0 6687 1598 0 t 0 0 9069 8251 2649 17258 17955 0 17955 0 15789 2600 9399 0
MA0482.1_shift3 (Gata4)		0.757	0.541	8.933	0.552	0.887	2.546	0.873	116	73	31	33	103	107	111	82.000	92	; oligos_6nt_mkv4_m4 versus MA0482.1 (Gata4); m=2/3; ncol2=11; w=10; offset=3; strand=D; shift=3; score= 82; ---yCTTATCTsyy ; cor=0.757; Ncor=0.541; logoDP=8.933; NIcor=0.552; NsEucl=0.887; SSD=2.546; NSW=0.873; rcor=116; rNcor=73; rlogoDP=31; rNIcor=33; rNsEucl=103; rSSD=107; rNSW=111; rank_mean=82.000; match_rank=92 a 0 0 0 10 0 0 0 2707 0 0 547 0 601 386 c 0 0 0 1039 2165 89 0 39 0 2746 0 1240 1004 929 g 0 0 0 374 306 0 0 0 0 0 0 940 157 682 t 0 0 0 1323 275 2657 2746 0 2746 0 2199 566 984 749
MA0037.2_rc_shift3 (GATA3_rc)		0.787	0.484	2.035	-0.076	0.867	2.253	0.859	86	94	106	109	121	84	122	103.143	122	; oligos_6nt_mkv4_m4 versus MA0037.2_rc (GATA3_rc); m=3/3; ncol2=8; w=8; offset=3; strand=R; shift=3; score=103.143; ---tYTTATCT--- ; cor=0.787; Ncor=0.484; logoDP=2.035; NIcor=-0.076; NsEucl=0.867; SSD=2.253; NSW=0.859; rcor=86; rNcor=94; rlogoDP=106; rNIcor=109; rNsEucl=121; rSSD=84; rNSW=122; rank_mean=103.143; match_rank=122 a 0 0 0 0 0 0 0 4628 0 0 0 0 0 0 c 0 0 0 1120 3338 0 0 0 0 4628 0 0 0 0 g 0 0 0 712 0 0 0 0 0 0 0 0 0 0 t 0 0 0 2796 1290 4628 4628 0 4628 0 4628 0 0 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m3_shift1 (positions_6nt_m3)																		; positions_6nt_m3; m=0 (reference); ncol1=13; shift=1; ncol=14; -rmAGTTGCAAAay ; Alignment reference a 0 115 113 342 0 0 0 0 0 343 342 344 223 67 c 0 76 100 2 0 0 1 0 344 0 0 0 27 93 g 0 90 71 0 344 0 0 344 0 1 0 0 50 71 t 0 63 60 0 0 344 343 0 0 0 2 0 44 113
MA0100.1_shift0 (Myb)		0.807	0.404	6.306	0.383	0.881	1.399	0.900	72	123	48	67	111	21	62	72.000	74	; positions_6nt_m3 versus MA0100.1 (Myb); m=1/4; ncol2=8; w=7; offset=-1; strand=D; shift=0; score= 72; grCvGTTG------ ; cor=0.807; Ncor=0.404; logoDP=6.306; NIcor=0.383; NsEucl=0.881; SSD=1.399; NSW=0.900; rcor=72; rNcor=123; rlogoDP=48; rNIcor=67; rNsEucl=111; rSSD=21; rNSW=62; rank_mean=72.000; match_rank=74 a 8 22 2 16 1 2 0 6 0 0 0 0 0 0 c 4 1 48 17 0 1 0 0 0 0 0 0 0 0 g 34 25 1 16 50 0 0 44 0 0 0 0 0 0 t 5 3 0 2 0 48 51 1 0 0 0 0 0 0
MA0102.3_shift4 (CEBPA)		0.770	0.550	8.677	0.520	0.886	2.590	0.870	105	69	33	43	104	110	115	82.714	96	; positions_6nt_m3 versus MA0102.3 (CEBPA); m=2/4; ncol2=11; w=10; offset=3; strand=D; shift=4; score=82.7143; ----aTTGCAyAAy ; cor=0.770; Ncor=0.550; logoDP=8.677; NIcor=0.520; NsEucl=0.886; SSD=2.590; NSW=0.870; rcor=105; rNcor=69; rlogoDP=33; rNIcor=43; rNsEucl=104; rSSD=110; rNSW=115; rank_mean=82.714; match_rank=96 a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826
MA0102.2_rc_shift4 (CEBPA_rc)		0.760	0.526	4.503	0.216	0.873	2.627	0.854	112	78	65	70	119	112	123	97.000	116	; positions_6nt_m3 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=3; strand=R; shift=4; score= 97; ----rTTGcrmaA- ; cor=0.760; Ncor=0.526; logoDP=4.503; NIcor=0.216; NsEucl=0.873; SSD=2.627; NSW=0.854; rcor=112; rNcor=78; rlogoDP=65; rNIcor=70; rNsEucl=119; rSSD=112; rNSW=123; rank_mean=97.000; match_rank=116 a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 t 0 0 0 0 0 18 18 2 4 2 4 1 3 0
MA0152.1_rc_shift6 (NFATC2_rc)		0.752	0.405	0.918	-0.050	0.852	2.141	0.847	120	121	109	106	124	76	124	111.429	124	; positions_6nt_m3 versus MA0152.1_rc (NFATC2_rc); m=4/4; ncol2=7; w=7; offset=5; strand=R; shift=6; score=111.429; ------TGGAAAA- ; cor=0.752; Ncor=0.405; logoDP=0.918; NIcor=-0.050; NsEucl=0.852; SSD=2.141; NSW=0.847; rcor=120; rNcor=121; rlogoDP=109; rNIcor=106; rNsEucl=124; rSSD=76; rNSW=124; rank_mean=111.429; match_rank=124 a 0 0 0 0 0 0 4 0 0 26 24 21 20 0 c 0 0 0 0 0 0 1 0 0 0 0 2 2 0 g 0 0 0 0 0 0 3 26 25 0 1 2 1 0 t 0 0 0 0 0 0 18 0 1 0 1 1 3 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m2_shift2 (oligos_7nt_mkv5_m2)																		; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=12; shift=2; ncol=15; --wwATTTTTAAaw- ; Alignment reference a 0 0 693 673 2588 0 0 0 0 0 2588 2586 1248 942 0 c 0 0 561 637 0 0 0 0 0 0 0 2 324 330 0 g 0 0 402 383 0 0 0 0 0 0 0 0 551 412 0 t 0 0 932 895 0 2588 2588 2588 2588 2588 0 0 465 904 0
MA0151.1_rc_shift7 (ARID3A_rc)		0.821	0.410	6.324	0.335	0.864	1.334	0.889	57	117	47	69	122	18	87	73.857	76	; oligos_7nt_mkv5_m2 versus MA0151.1_rc (ARID3A_rc); m=1/2; ncol2=6; w=6; offset=5; strand=R; shift=7; score=73.8571; -------TTTrAT-- ; cor=0.821; Ncor=0.410; logoDP=6.324; NIcor=0.335; NsEucl=0.864; SSD=1.334; NSW=0.889; rcor=57; rNcor=117; rlogoDP=47; rNIcor=69; rNsEucl=122; rSSD=18; rNSW=87; rank_mean=73.857; match_rank=76 a 0 0 0 0 0 0 0 6 0 0 17 27 0 0 0 c 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 t 0 0 0 0 0 0 0 20 27 27 1 0 27 0 0
MA0497.1_rc_shift0 (MEF2C_rc)		0.752	0.601	2.162	-0.067	0.901	2.817	0.883	122	46	103	108	63	119	96	93.857	113	; oligos_7nt_mkv5_m2 versus MA0497.1_rc (MEF2C_rc); m=2/2; ncol2=15; w=12; offset=-2; strand=R; shift=0; score=93.8571; wkCTATTTTTrgmhy ; cor=0.752; Ncor=0.601; logoDP=2.162; NIcor=-0.067; NsEucl=0.901; SSD=2.817; NSW=0.883; rcor=122; rNcor=46; rlogoDP=103; rNIcor=108; rNsEucl=63; rSSD=119; rNSW=96; rank_mean=93.857; match_rank=113 a 624 250 29 0 2091 70 76 15 230 263 1224 337 760 752 507 c 126 148 1671 32 0 4 2 87 241 74 0 78 822 573 676 g 450 836 120 0 62 0 0 0 32 256 985 1412 196 151 321 t 1009 975 389 2177 56 2135 2131 2107 1706 1616 0 382 431 733 705

One-to-n matrix alignment; reference matrix: positions_8nt_m5_shift0 ; 4 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_8nt_m5_shift0 (positions_8nt_m5)																		; positions_8nt_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; rwATGTTGCAATCATtw ; Alignment reference a 51 42 154 1 0 17 1 1 7 163 165 3 8 146 9 41 46 c 33 31 4 1 2 3 4 1 152 2 0 3 152 7 13 38 40 g 45 38 7 0 155 2 5 164 1 0 0 3 2 3 10 36 34 t 37 55 1 164 9 144 156 0 6 1 1 157 4 10 134 51 46
MA0102.3_rc_shift1 (CEBPA_rc)		0.798	0.516	4.406	0.116	0.900	2.401	0.891	82	82	67	84	66	95	81	79.571	89	; positions_8nt_m5 versus MA0102.3_rc (CEBPA_rc); m=1/3; ncol2=11; w=11; offset=1; strand=R; shift=1; score=79.5714; -krTTrTGCAAt----- ; cor=0.798; Ncor=0.516; logoDP=4.406; NIcor=0.116; NsEucl=0.900; SSD=2.401; NSW=0.891; rcor=82; rNcor=82; rlogoDP=67; rNIcor=84; rNsEucl=66; rSSD=95; rNSW=81; rank_mean=79.571; match_rank=89 a 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0 0 c 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0 0 g 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0 0 t 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0 0
MA0466.1_rc_shift2 (CEBPB_rc)		0.814	0.526	2.312	-0.065	0.900	2.409	0.891	64	77	102	107	68	99	84	85.857	102	; positions_8nt_m5 versus MA0466.1_rc (CEBPB_rc); m=2/3; ncol2=11; w=11; offset=2; strand=R; shift=2; score=85.8571; --rTkrTGCAATm---- ; cor=0.814; Ncor=0.526; logoDP=2.312; NIcor=-0.065; NsEucl=0.900; SSD=2.409; NSW=0.891; rcor=64; rNcor=77; rlogoDP=102; rNIcor=107; rNsEucl=68; rSSD=99; rNSW=84; rank_mean=85.857; match_rank=102 a 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 0 c 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 0 g 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 0 t 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0 0
MA0102.2_shift3 (CEBPA)		0.761	0.403	5.949	0.375	0.876	2.497	0.861	111	124	64	68	118	104	121	101.429	121	; positions_8nt_m5 versus MA0102.2 (CEBPA); m=3/3; ncol2=9; w=9; offset=3; strand=D; shift=3; score=101.429; ---TtkygCAAy----- ; cor=0.761; Ncor=0.403; logoDP=5.949; NIcor=0.375; NsEucl=0.876; SSD=2.497; NSW=0.861; rcor=111; rNcor=124; rlogoDP=64; rNIcor=68; rNsEucl=118; rSSD=104; rNSW=121; rank_mean=101.429; match_rank=121 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m2_shift0 (dyads_m2)																		; dyads_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; taAWTAAATAAATAAAw ; Alignment reference a 169 428 683 502 27 709 718 719 19 722 721 719 5 714 717 592 306 c 112 46 25 9 9 3 3 1 2 1 1 1 6 1 0 22 54 g 29 179 5 25 3 5 2 4 4 0 2 3 0 5 3 52 41 t 415 72 12 189 686 8 2 1 700 2 1 2 714 5 5 59 324
MA0042.1_rc_shift5 (FOXI1_rc)		0.783	0.553	4.476	0.115	0.898	3.020	0.874	90	67	66	85	75	122	108	87.571	105	; dyads_m2 versus MA0042.1_rc (FOXI1_rc); m=1/1; ncol2=12; w=12; offset=5; strand=R; shift=5; score=87.5714; -----AwAyAAAyAhsm ; cor=0.783; Ncor=0.553; logoDP=4.476; NIcor=0.115; NsEucl=0.898; SSD=3.020; NSW=0.874; rcor=90; rNcor=67; rlogoDP=66; rNIcor=85; rNsEucl=75; rSSD=122; rNSW=108; rank_mean=87.571; match_rank=105 a 0 0 0 0 0 24 18 24 0 31 31 31 0 31 8 7 10 c 0 0 0 0 0 4 4 7 16 0 0 0 18 0 8 12 14 g 0 0 0 0 0 1 1 0 0 0 0 0 0 0 4 8 1 t 0 0 0 0 0 2 8 0 15 0 0 0 13 0 11 4 6

One-to-n matrix alignment; reference matrix: dyads_m4_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
dyads_m4_shift0 (dyads_m4)																		; dyads_m4; m=0 (reference); ncol1=16; shift=0; ncol=16; awyAAATAAATAAAww ; Alignment reference a 816 878 261 1523 1525 1523 37 1539 1545 1536 17 1531 1527 1524 565 769 c 357 125 635 13 8 9 27 9 9 8 28 11 20 10 156 222 g 180 136 26 10 26 21 21 13 8 19 16 16 8 12 105 130 t 214 428 645 21 8 14 1482 6 5 4 1506 9 12 21 741 446
MA0042.1_rc_shift3 (FOXI1_rc)		0.772	0.579	4.114	0.117	0.895	3.146	0.869	101	54	73	83	80	123	117	90.143	108	; dyads_m4 versus MA0042.1_rc (FOXI1_rc); m=1/1; ncol2=12; w=12; offset=3; strand=R; shift=3; score=90.1429; ---AwAyAAAyAhsm- ; cor=0.772; Ncor=0.579; logoDP=4.114; NIcor=0.117; NsEucl=0.895; SSD=3.146; NSW=0.869; rcor=101; rNcor=54; rlogoDP=73; rNIcor=83; rNsEucl=80; rSSD=123; rNSW=117; rank_mean=90.143; match_rank=108 a 0 0 0 24 18 24 0 31 31 31 0 31 8 7 10 0 c 0 0 0 4 4 7 16 0 0 0 18 0 8 12 14 0 g 0 0 0 1 1 0 0 0 0 0 0 0 4 8 1 0 t 0 0 0 2 8 0 15 0 0 0 13 0 11 4 6 0

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2)																		; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=0; ncol=11; waCAAAACww- ; Alignment reference a 3660 3670 0 9696 9696 9696 9696 0 4475 3410 0 c 1400 1795 9696 0 0 0 0 9696 1982 2007 0 g 1654 1877 0 0 0 0 0 0 512 1854 0 t 2982 2354 0 0 0 0 0 0 2727 2425 0
MA0087.1_rc_shift4 (Sox5_rc)		0.766	0.418	1.994	0.014	0.855	1.518	0.874	108	114	107	102	123	27	109	98.571	118	; oligos_6nt_mkv4_m2 versus MA0087.1_rc (Sox5_rc); m=1/1; ncol2=7; w=6; offset=4; strand=R; shift=4; score=98.5714; ----wAACAAT ; cor=0.766; Ncor=0.418; logoDP=1.994; NIcor=0.014; NsEucl=0.855; SSD=1.518; NSW=0.874; rcor=108; rNcor=114; rlogoDP=107; rNIcor=102; rNsEucl=123; rSSD=27; rNSW=109; rank_mean=98.571; match_rank=118 a 0 0 0 0 8 21 22 0 23 22 0 c 0 0 0 0 4 0 0 22 0 1 0 g 0 0 0 0 3 1 1 0 0 0 0 t 0 0 0 0 8 1 0 1 0 0 23