One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB.tab

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=20; shift=0; ncol=20; wwwTTGATctadATCAAwww ; Alignment reference a 13 17 18 2 0 2 26 0 6 5 16 7 25 1 0 28 26 9 9 7 c 3 2 2 0 0 0 0 3 13 3 2 5 1 0 25 0 0 0 2 5 g 5 1 0 0 0 26 0 1 3 3 4 9 2 0 0 0 0 3 2 5 t 7 8 8 26 28 0 2 24 6 17 6 7 0 27 3 0 2 16 15 11
3061_FNR_RegulonDB_7.5__shift3 (3061_FNR_RegulonDB_7.5_)		0.948	0.663	6.730	0.655	0.954	0.822	0.971	2	7	39	5	1	9	2	9.286	1	; dyads_m1 versus 3061_FNR_RegulonDB_7.5_; m=1/2; ncol2=14; w=14; offset=3; strand=D; shift=3; score= 9.2857; ---tTGaTywayATCAA--- ; cor=0.948; Ncor=0.663; logoDP=6.730; NIcor=0.655; NsEucl=0.954; SSD=0.822; NSW=0.971; rcor=2; rNcor=7; rlogoDP=39; rNIcor=5; rNsEucl=1; rSSD=9; rNSW=2; rank_mean=9.286; match_rank=1 a 0 0 0 17 5 13 47 10 17 28 48 20 66 4 0 80 73 0 0 0 c 0 0 0 8 8 10 14 3 28 10 12 23 0 0 72 1 8 0 0 0 g 0 0 0 10 6 58 8 13 3 16 11 11 11 0 5 0 0 0 0 0 t 0 0 0 48 64 2 14 57 35 29 12 29 6 79 6 2 2 0 0 0
7440_HNF6_f1_HOCOMOCO_v9__rc_shift7 (7440_HNF6_f1_HOCOMOCO_v9__rc)		0.780	0.507	1.034	-0.102	0.922	2.080	0.920	51	31	72	75	14	54	24	45.857	46	; dyads_m1 versus 7440_HNF6_f1_HOCOMOCO_v9__rc; m=2/2; ncol2=13; w=13; offset=7; strand=R; shift=7; score=45.8571; -------whwaARTCAATAw ; cor=0.780; Ncor=0.507; logoDP=1.034; NIcor=-0.102; NsEucl=0.922; SSD=2.080; NSW=0.920; rcor=51; rNcor=31; rlogoDP=72; rNIcor=75; rNsEucl=14; rSSD=54; rNSW=24; rank_mean=45.857; match_rank=46 a 0 0 0 0 0 0 0 9 9 11 16 19 17 0 0 20 24 0 17 13 c 0 0 0 0 0 0 0 3 7 2 0 2 0 1 24 3 0 0 1 0 g 0 0 0 0 0 0 0 5 2 3 3 1 7 0 0 1 0 0 4 4 t 0 0 0 0 0 0 0 7 6 8 5 2 0 23 0 0 0 24 2 7

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 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
dyads_m2_shift0 (dyads_m2)																		; dyads_m2; m=0 (reference); ncol1=20; shift=0; ncol=24; wwwTTGAystagATCAAtww---- ; Alignment reference a 12 8 11 1 0 3 27 0 6 6 15 5 26 2 0 28 26 4 11 9 0 0 0 0 c 4 5 4 0 1 0 0 12 9 4 3 5 1 0 26 0 2 0 2 1 0 0 0 0 g 3 3 4 1 0 25 0 3 7 3 5 14 1 0 0 0 0 5 0 5 0 0 0 0 t 9 12 9 26 27 0 1 13 6 15 5 4 0 26 2 0 0 19 15 13 0 0 0 0
3061_FNR_RegulonDB_7.5__rc_shift3 (3061_FNR_RegulonDB_7.5__rc)		0.915	0.641	6.428	0.637	0.948	1.060	0.962	10	9	41	6	2	14	5	12.429	2	; dyads_m2 versus 3061_FNR_RegulonDB_7.5__rc; m=1/8; ncol2=14; w=14; offset=3; strand=R; shift=3; score=12.4286; ---TTGATrtwrAtCAa------- ; cor=0.915; Ncor=0.641; logoDP=6.428; NIcor=0.637; NsEucl=0.948; SSD=1.060; NSW=0.962; rcor=10; rNcor=9; rlogoDP=41; rNIcor=6; rNsEucl=2; rSSD=14; rNSW=5; rank_mean=12.429; match_rank=2 a 0 0 0 2 2 6 79 6 29 12 29 35 57 14 2 64 48 0 0 0 0 0 0 0 c 0 0 0 0 0 5 0 11 11 11 16 3 13 8 58 6 10 0 0 0 0 0 0 0 g 0 0 0 8 1 72 0 0 23 12 10 28 3 14 10 8 8 0 0 0 0 0 0 0 t 0 0 0 73 80 0 4 66 20 48 28 17 10 47 13 5 17 0 0 0 0 0 0 0
1999_PB0144.1_JASPAR_CORE_2009__shift8 (1999_PB0144.1_JASPAR_CORE_2009_)		0.839	0.420	5.565	0.431	0.932	1.343	0.944	26	66	49	32	5	24	11	30.429	17	; dyads_m2 versus 1999_PB0144.1_JASPAR_CORE_2009_; m=2/8; ncol2=16; w=12; offset=8; strand=D; shift=8; score=30.4286; --------swrsATCAATCrctww ; cor=0.839; Ncor=0.420; logoDP=5.565; NIcor=0.431; NsEucl=0.932; SSD=1.343; NSW=0.944; rcor=26; rNcor=66; rlogoDP=49; rNIcor=32; rNsEucl=5; rSSD=24; rNSW=11; rank_mean=30.429; match_rank=17 a 0 0 0 0 0 0 0 0 23 44 42 17 81 4 2 94 93 3 11 68 24 9 33 34 c 0 0 0 0 0 0 0 0 27 8 14 34 2 1 90 1 1 2 71 2 35 24 18 16 g 0 0 0 0 0 0 0 0 39 23 32 39 1 1 4 1 4 5 1 28 19 20 11 19 t 0 0 0 0 0 0 0 0 11 25 12 10 16 94 4 4 2 91 17 3 23 46 38 32
2042_PB0188.1_JASPAR_CORE_2009__shift8 (2042_PB0188.1_JASPAR_CORE_2009_)		0.832	0.416	5.073	0.430	0.932	1.342	0.944	27	72	50	35	4	23	10	31.571	19	; dyads_m2 versus 2042_PB0188.1_JASPAR_CORE_2009_; m=3/8; ncol2=16; w=12; offset=8; strand=D; shift=8; score=31.5714; --------sdrsWTCAATCrstww ; cor=0.832; Ncor=0.416; logoDP=5.073; NIcor=0.430; NsEucl=0.932; SSD=1.342; NSW=0.944; rcor=27; rNcor=72; rlogoDP=50; rNIcor=35; rNsEucl=4; rSSD=23; rNSW=10; rank_mean=31.571; match_rank=19 a 0 0 0 0 0 0 0 0 22 34 40 24 70 5 2 93 93 3 12 59 14 12 36 33 c 0 0 0 0 0 0 0 0 30 5 16 26 3 2 85 1 1 2 69 2 38 18 20 17 g 0 0 0 0 0 0 0 0 37 34 35 39 1 1 6 1 3 5 1 36 27 24 11 20 t 0 0 0 0 0 0 0 0 12 27 10 10 26 92 7 5 2 90 18 4 21 46 33 30
1000_UP00185_UniPROBE_20120919__shift6 (1000_UP00185_UniPROBE_20120919_)		0.765	0.466	5.022	0.471	0.927	2.111	0.925	65	44	51	24	6	57	19	38.000	30	; dyads_m2 versus 1000_UP00185_UniPROBE_20120919_; m=4/8; ncol2=17; w=14; offset=6; strand=D; shift=6; score= 38; ------yyaymCATCAAwmwwmm- ; cor=0.765; Ncor=0.466; logoDP=5.022; NIcor=0.471; NsEucl=0.927; SSD=2.111; NSW=0.925; rcor=65; rNcor=44; rlogoDP=51; rNIcor=24; rNsEucl=6; rSSD=57; rNSW=19; rank_mean=38.000; match_rank=30 a 0 0 0 0 0 0 21 6 59 12 37 11 86 3 3 93 74 31 32 39 36 26 37 0 c 0 0 0 0 0 0 28 50 4 40 39 73 2 1 95 3 6 5 32 14 13 29 35 0 g 0 0 0 0 0 0 15 15 14 9 11 9 7 1 1 2 3 6 15 9 15 24 21 0 t 0 0 0 0 0 0 36 29 23 39 13 7 5 95 1 2 17 58 21 38 36 21 7 0
7440_HNF6_f1_HOCOMOCO_v9__rc_shift7 (7440_HNF6_f1_HOCOMOCO_v9__rc)		0.805	0.524	0.878	-0.127	0.927	1.821	0.930	35	20	75	79	7	39	16	38.714	31	; dyads_m2 versus 7440_HNF6_f1_HOCOMOCO_v9__rc; m=5/8; ncol2=13; w=13; offset=7; strand=R; shift=7; score=38.7143; -------whwaARTCAATAw---- ; cor=0.805; Ncor=0.524; logoDP=0.878; NIcor=-0.127; NsEucl=0.927; SSD=1.821; NSW=0.930; rcor=35; rNcor=20; rlogoDP=75; rNIcor=79; rNsEucl=7; rSSD=39; rNSW=16; rank_mean=38.714; match_rank=31 a 0 0 0 0 0 0 0 9 9 11 16 19 17 0 0 20 24 0 17 13 0 0 0 0 c 0 0 0 0 0 0 0 3 7 2 0 2 0 1 24 3 0 0 1 0 0 0 0 0 g 0 0 0 0 0 0 0 5 2 3 3 1 7 0 0 1 0 0 4 4 0 0 0 0 t 0 0 0 0 0 0 0 7 6 8 5 2 0 23 0 0 0 24 2 7 0 0 0 0
2984_PH0134.1_JASPAR_CORE_2009__shift6 (2984_PH0134.1_JASPAR_CORE_2009_)		0.764	0.465	5.021	0.471	0.926	2.119	0.924	69	45	52	25	8	58	20	39.571	36	; dyads_m2 versus 2984_PH0134.1_JASPAR_CORE_2009_; m=6/8; ncol2=17; w=14; offset=6; strand=D; shift=6; score=39.5714; ------yyaymCATCAAwmwwmm- ; cor=0.764; Ncor=0.465; logoDP=5.021; NIcor=0.471; NsEucl=0.926; SSD=2.119; NSW=0.924; rcor=69; rNcor=45; rlogoDP=52; rNIcor=25; rNsEucl=8; rSSD=58; rNSW=20; rank_mean=39.571; match_rank=36 a 0 0 0 0 0 0 21 6 59 12 37 11 86 3 3 93 74 31 32 39 36 26 37 0 c 0 0 0 0 0 0 28 49 3 40 39 73 2 1 95 3 6 5 32 14 14 29 35 0 g 0 0 0 0 0 0 15 15 14 9 11 9 7 1 1 2 3 6 15 9 15 24 21 0 t 0 0 0 0 0 0 36 29 23 39 13 7 5 95 1 2 17 58 21 38 36 21 7 0
1924_PB0063.1_JASPAR_CORE_2009__shift7 (1924_PB0063.1_JASPAR_CORE_2009_)		0.750	0.424	4.768	0.416	0.921	2.123	0.918	88	64	56	45	15	59	27	50.571	59	; dyads_m2 versus 1924_PB0063.1_JASPAR_CORE_2009_; m=7/8; ncol2=16; w=13; offset=7; strand=D; shift=7; score=50.5714; -------wtwrgAACAATwwwtw- ; cor=0.750; Ncor=0.424; logoDP=4.768; NIcor=0.416; NsEucl=0.921; SSD=2.123; NSW=0.918; rcor=88; rNcor=64; rlogoDP=56; rNIcor=45; rNsEucl=15; rSSD=59; rNSW=27; rank_mean=50.571; match_rank=59 a 0 0 0 0 0 0 0 27 19 37 50 13 83 96 2 94 95 4 47 42 36 21 30 0 c 0 0 0 0 0 0 0 12 24 14 11 9 2 1 90 1 1 3 2 9 10 20 16 0 g 0 0 0 0 0 0 0 17 18 16 28 62 13 1 1 1 3 1 8 12 18 12 7 0 t 0 0 0 0 0 0 0 44 40 33 11 16 3 2 7 4 1 93 44 38 36 47 46 0
3793_UP00096_UniPROBE_20120919__shift7 (3793_UP00096_UniPROBE_20120919_)		0.750	0.424	4.822	0.416	0.921	2.131	0.918	86	63	54	46	16	61	28	50.571	60	; dyads_m2 versus 3793_UP00096_UniPROBE_20120919_; m=8/8; ncol2=16; w=13; offset=7; strand=D; shift=7; score=50.5714; -------wtwrgAACAATwwwtw- ; cor=0.750; Ncor=0.424; logoDP=4.822; NIcor=0.416; NsEucl=0.921; SSD=2.131; NSW=0.918; rcor=86; rNcor=63; rlogoDP=54; rNIcor=46; rNsEucl=16; rSSD=61; rNSW=28; rank_mean=50.571; match_rank=60 a 0 0 0 0 0 0 0 27 18 37 50 13 83 96 2 94 95 3 47 42 36 21 30 0 c 0 0 0 0 0 0 0 12 24 14 11 9 1 1 90 1 1 3 2 9 10 20 17 0 g 0 0 0 0 0 0 0 17 18 16 28 62 13 1 1 1 3 1 7 12 18 12 7 0 t 0 0 0 0 0 0 0 44 40 33 11 16 3 2 7 4 1 93 44 37 36 47 46 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_shift8 ; 36 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_mkv2_shift8 (oligos_6nt_mkv2)																		; oligos_6nt_mkv2; m=0 (reference); ncol1=11; shift=8; ncol=19; --------taGATCAATrw ; Alignment reference a 0 0 0 0 0 0 0 0 1 2 0 5 0 0 5 5 0 3 2 c 0 0 0 0 0 0 0 0 1 1 0 0 0 5 0 0 0 0 0 g 0 0 0 0 0 0 0 0 1 1 5 0 0 0 0 0 0 2 1 t 0 0 0 0 0 0 0 0 2 1 0 0 5 0 0 0 5 0 2
2784_PF0097.1_JASPAR_CORE_2009__rc_shift10 (2784_PF0097.1_JASPAR_CORE_2009__rc)		0.916	0.666	7.697	0.346	0.917	0.885	0.945	9	6	27	59	17	11	9	19.714	3	; oligos_6nt_mkv2 versus 2784_PF0097.1_JASPAR_CORE_2009__rc; m=1/35; ncol2=8; w=8; offset=2; strand=R; shift=10; score=19.7143; ----------GATrAATr- ; cor=0.916; Ncor=0.666; logoDP=7.697; NIcor=0.346; NsEucl=0.917; SSD=0.885; NSW=0.945; rcor=9; rNcor=6; rlogoDP=27; rNIcor=59; rNsEucl=17; rSSD=11; rNSW=9; rank_mean=19.714; match_rank=3 a 0 0 0 0 0 0 0 0 0 0 0 992 0 360 992 992 0 533 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 195 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 992 0 0 259 0 0 0 459 0 t 0 0 0 0 0 0 0 0 0 0 0 0 992 178 0 0 992 0 0
7424_HBP1_f1_HOCOMOCO_v9__shift13 (7424_HBP1_f1_HOCOMOCO_v9_)		0.939	0.433	6.895	0.434	0.925	0.400	0.967	4	56	34	31	10	2	4	20.143	4	; oligos_6nt_mkv2 versus 7424_HBP1_f1_HOCOMOCO_v9_; m=2/35; ncol2=8; w=6; offset=5; strand=D; shift=13; score=20.1429; -------------CAATgr ; cor=0.939; Ncor=0.433; logoDP=6.895; NIcor=0.434; NsEucl=0.925; SSD=0.400; NSW=0.967; rcor=4; rNcor=56; rlogoDP=34; rNIcor=31; rNsEucl=10; rSSD=2; rNSW=4; rank_mean=20.143; match_rank=4 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 5 0 1 2 c 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 1 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 3 2 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 1
6530_3a01_E_3D-footprint_20130124__shift13 (6530_3a01_E_3D-footprint_20130124_)		0.896	0.489	7.801	0.504	0.901	0.712	0.941	11	36	23	21	37	5	12	20.714	5	; oligos_6nt_mkv2 versus 6530_3a01_E_3D-footprint_20130124_; m=3/35; ncol2=6; w=6; offset=5; strand=D; shift=13; score=20.7143; -------------CAATtA ; cor=0.896; Ncor=0.489; logoDP=7.801; NIcor=0.504; NsEucl=0.901; SSD=0.712; NSW=0.941; rcor=11; rNcor=36; rlogoDP=23; rNIcor=21; rNsEucl=37; rSSD=5; rNSW=12; rank_mean=20.714; match_rank=5 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 96 96 0 20 77 c 0 0 0 0 0 0 0 0 0 0 0 0 0 96 0 0 0 19 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 19 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 96 38 0
5766_SOX18_full_2_HumanTF_1.0__shift11 (5766_SOX18_full_2_HumanTF_1.0_)		0.921	0.410	10.470	0.424	0.924	0.743	0.954	7	81	3	40	13	8	8	22.857	6	; oligos_6nt_mkv2 versus 5766_SOX18_full_2_HumanTF_1.0_; m=4/35; ncol2=15; w=8; offset=3; strand=D; shift=11; score=22.8571; -----------ATCAATwk ; cor=0.921; Ncor=0.410; logoDP=10.470; NIcor=0.424; NsEucl=0.924; SSD=0.743; NSW=0.954; rcor=7; rNcor=81; rlogoDP=3; rNIcor=40; rNsEucl=13; rSSD=8; rNSW=8; rank_mean=22.857; match_rank=6 a 0 0 0 0 0 0 0 0 0 0 0 298 8 0 298 298 0 96 51 c 0 0 0 0 0 0 0 0 0 0 0 14 0 298 0 0 0 7 36 g 0 0 0 0 0 0 0 0 0 0 0 31 0 0 0 0 0 15 132 t 0 0 0 0 0 0 0 0 0 0 0 6 298 0 0 0 298 180 78
5763_SOX15_full_2_HumanTF_1.0__shift11 (5763_SOX15_full_2_HumanTF_1.0_)		0.925	0.411	10.378	0.414	0.924	0.730	0.954	6	78	4	49	12	7	7	23.286	7	; oligos_6nt_mkv2 versus 5763_SOX15_full_2_HumanTF_1.0_; m=5/35; ncol2=15; w=8; offset=3; strand=D; shift=11; score=23.2857; -----------ATCAATAm ; cor=0.925; Ncor=0.411; logoDP=10.378; NIcor=0.414; NsEucl=0.924; SSD=0.730; NSW=0.954; rcor=6; rNcor=78; rlogoDP=4; rNIcor=49; rNsEucl=12; rSSD=7; rNSW=7; rank_mean=23.286; match_rank=7 a 0 0 0 0 0 0 0 0 0 0 0 88 0 0 88 88 0 88 88 c 0 0 0 0 0 0 0 0 0 0 0 28 3 88 0 3 0 0 37 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 3 88 0 0 0 88 5 6
1999_PB0144.1_JASPAR_CORE_2009__shift7 (1999_PB0144.1_JASPAR_CORE_2009_)		0.818	0.562	7.711	0.585	0.911	1.897	0.914	32	15	26	10	20	42	31	25.143	8	; oligos_6nt_mkv2 versus 1999_PB0144.1_JASPAR_CORE_2009_; m=6/35; ncol2=16; w=11; offset=-1; strand=D; shift=7; score=25.1429; -------swrsATCAATCr ; cor=0.818; Ncor=0.562; logoDP=7.711; NIcor=0.585; NsEucl=0.911; SSD=1.897; NSW=0.914; rcor=32; rNcor=15; rlogoDP=26; rNIcor=10; rNsEucl=20; rSSD=42; rNSW=31; rank_mean=25.143; match_rank=8 a 0 0 0 0 0 0 0 23 44 42 17 81 4 2 94 93 3 11 68 c 0 0 0 0 0 0 0 27 8 14 34 2 1 90 1 1 2 71 2 g 0 0 0 0 0 0 0 39 23 32 39 1 1 4 1 4 5 1 28 t 0 0 0 0 0 0 0 11 25 12 10 16 94 4 4 2 91 17 3
5829_Sox3_DBD_2_HumanTF_1.0__shift10 (5829_Sox3_DBD_2_HumanTF_1.0_)		0.884	0.419	10.178	0.419	0.913	1.236	0.931	15	67	7	42	19	20	15	26.429	10	; oligos_6nt_mkv2 versus 5829_Sox3_DBD_2_HumanTF_1.0_; m=7/35; ncol2=17; w=9; offset=2; strand=D; shift=10; score=26.4286; ----------sATCAATGt ; cor=0.884; Ncor=0.419; logoDP=10.178; NIcor=0.419; NsEucl=0.913; SSD=1.236; NSW=0.931; rcor=15; rNcor=67; rlogoDP=7; rNIcor=42; rNsEucl=19; rSSD=20; rNSW=15; rank_mean=26.429; match_rank=10 a 0 0 0 0 0 0 0 0 0 0 113 1477 54 0 1477 1477 0 0 103 c 0 0 0 0 0 0 0 0 0 0 459 96 1 1477 0 0 1 0 226 g 0 0 0 0 0 0 0 0 0 0 623 197 7 2 1 1 0 1116 352 t 0 0 0 0 0 0 0 0 0 0 282 98 1477 10 0 0 1477 361 796
2042_PB0188.1_JASPAR_CORE_2009__shift7 (2042_PB0188.1_JASPAR_CORE_2009_)		0.814	0.559	7.045	0.586	0.911	1.923	0.913	33	16	33	9	21	43	32	26.714	11	; oligos_6nt_mkv2 versus 2042_PB0188.1_JASPAR_CORE_2009_; m=8/35; ncol2=16; w=11; offset=-1; strand=D; shift=7; score=26.7143; -------sdrsWTCAATCr ; cor=0.814; Ncor=0.559; logoDP=7.045; NIcor=0.586; NsEucl=0.911; SSD=1.923; NSW=0.913; rcor=33; rNcor=16; rlogoDP=33; rNIcor=9; rNsEucl=21; rSSD=43; rNSW=32; rank_mean=26.714; match_rank=11 a 0 0 0 0 0 0 0 22 34 40 24 70 5 2 93 93 3 12 59 c 0 0 0 0 0 0 0 30 5 16 26 3 2 85 1 1 2 69 2 g 0 0 0 0 0 0 0 37 34 35 39 1 1 6 1 3 5 1 36 t 0 0 0 0 0 0 0 12 27 10 10 26 92 7 5 2 90 18 4
5774_SOX2_DBD_3_HumanTF_1.0__shift10 (5774_SOX2_DBD_3_HumanTF_1.0_)		0.886	0.420	10.258	0.408	0.913	1.212	0.933	14	65	6	52	18	18	14	26.714	12	; oligos_6nt_mkv2 versus 5774_SOX2_DBD_3_HumanTF_1.0_; m=9/35; ncol2=17; w=9; offset=2; strand=D; shift=10; score=26.7143; ----------rATCAATGk ; cor=0.886; Ncor=0.420; logoDP=10.258; NIcor=0.408; NsEucl=0.913; SSD=1.212; NSW=0.933; rcor=14; rNcor=65; rlogoDP=6; rNIcor=52; rNsEucl=18; rSSD=18; rNSW=14; rank_mean=26.714; match_rank=12 a 0 0 0 0 0 0 0 0 0 0 105 352 7 0 352 352 0 19 49 c 0 0 0 0 0 0 0 0 0 0 62 17 2 352 0 0 0 0 55 g 0 0 0 0 0 0 0 0 0 0 131 56 7 0 0 0 0 296 115 t 0 0 0 0 0 0 0 0 0 0 54 17 352 0 0 0 352 38 132
5048_ZmHOX2a_2__Athamap_20091028__rc_shift8 (5048_ZmHOX2a_2__Athamap_20091028__rc)		0.926	0.589	0.139	-0.157	0.926	0.543	0.961	5	11	83	82	9	4	6	28.571	15	; oligos_6nt_mkv2 versus 5048_ZmHOX2a_2__Athamap_20091028__rc; m=10/35; ncol2=7; w=7; offset=0; strand=R; shift=8; score=28.5714; --------cmGATCa---- ; cor=0.926; Ncor=0.589; logoDP=0.139; NIcor=-0.157; NsEucl=0.926; SSD=0.543; NSW=0.961; rcor=5; rNcor=11; rlogoDP=83; rNIcor=82; rNsEucl=9; rSSD=4; rNSW=6; rank_mean=28.571; match_rank=15 a 0 0 0 0 0 0 0 0 6 16 0 27 0 0 15 0 0 0 0 c 0 0 0 0 0 0 0 0 14 7 0 0 0 27 5 0 0 0 0 g 0 0 0 0 0 0 0 0 4 4 27 0 0 0 2 0 0 0 0 t 0 0 0 0 0 0 0 0 3 0 0 0 27 0 5 0 0 0 0
5197_CUX1_DBD_3_HumanTF_1.0__shift9 (5197_CUX1_DBD_3_HumanTF_1.0_)		0.792	0.720	9.238	0.710	0.896	2.148	0.893	47	1	11	3	44	63	52	31.571	18	; oligos_6nt_mkv2 versus 5197_CUX1_DBD_3_HumanTF_1.0_; m=11/35; ncol2=10; w=10; offset=1; strand=D; shift=9; score=31.5714; ---------TrATCrATam ; cor=0.792; Ncor=0.720; logoDP=9.238; NIcor=0.710; NsEucl=0.896; SSD=2.148; NSW=0.893; rcor=47; rNcor=1; rlogoDP=11; rNIcor=3; rNsEucl=44; rSSD=63; rNSW=52; rank_mean=31.571; match_rank=18 a 0 0 0 0 0 0 0 0 0 4099 25659 25659 71 51 9580 25659 150 25659 8168 c 0 0 0 0 0 0 0 0 0 4649 3296 109 294 25659 264 45 95 9420 7633 g 0 0 0 0 0 0 0 0 0 2401 15550 192 77 53 16079 85 29 7560 3958 t 0 0 0 0 0 0 0 0 0 25659 7605 167 25659 595 130 231 25659 7079 5900
2653_MA0434.1_JASPAR_CORE_2009__shift6 (2653_MA0434.1_JASPAR_CORE_2009_)		0.845	0.455	6.405	0.438	0.894	1.100	0.921	25	48	42	30	45	16	23	32.714	21	; oligos_6nt_mkv2 versus 2653_MA0434.1_JASPAR_CORE_2009_; m=12/35; ncol2=9; w=7; offset=-2; strand=D; shift=6; score=32.7143; ------yGymrATCm---- ; cor=0.845; Ncor=0.455; logoDP=6.405; NIcor=0.438; NsEucl=0.894; SSD=1.100; NSW=0.921; rcor=25; rNcor=48; rlogoDP=42; rNIcor=30; rNsEucl=45; rSSD=16; rNSW=23; rank_mean=32.714; match_rank=21 a 0 0 0 0 0 0 11 0 9 63 40 100 0 0 36 0 0 0 0 c 0 0 0 0 0 0 36 0 26 26 0 0 0 100 30 0 0 0 0 g 0 0 0 0 0 0 11 100 0 0 60 0 0 0 17 0 0 0 0 t 0 0 0 0 0 0 41 0 65 11 0 0 100 0 17 0 0 0 0
5776_SOX2_full_2_HumanTF_1.0__rc_shift10 (5776_SOX2_full_2_HumanTF_1.0__rc)		0.870	0.412	9.016	0.406	0.907	1.399	0.922	17	77	12	53	22	30	22	33.286	22	; oligos_6nt_mkv2 versus 5776_SOX2_full_2_HumanTF_1.0__rc; m=13/35; ncol2=17; w=9; offset=2; strand=R; shift=10; score=33.2857; ----------kATCAATGk ; cor=0.870; Ncor=0.412; logoDP=9.016; NIcor=0.406; NsEucl=0.907; SSD=1.399; NSW=0.922; rcor=17; rNcor=77; rlogoDP=12; rNIcor=53; rNsEucl=22; rSSD=30; rNSW=22; rank_mean=33.286; match_rank=22 a 0 0 0 0 0 0 0 0 0 0 17 85 1 0 85 85 0 4 11 c 0 0 0 0 0 0 0 0 0 0 3 4 0 85 0 0 0 0 14 g 0 0 0 0 0 0 0 0 0 0 29 6 0 0 0 0 0 85 25 t 0 0 0 0 0 0 0 0 0 0 36 1 85 0 0 0 85 0 35
5199_CUX2_DBD_2_HumanTF_1.0__shift9 (5199_CUX2_DBD_2_HumanTF_1.0_)		0.768	0.698	8.936	0.681	0.890	2.407	0.880	61	3	13	4	50	80	61	38.857	32	; oligos_6nt_mkv2 versus 5199_CUX2_DBD_2_HumanTF_1.0_; m=14/35; ncol2=10; w=10; offset=1; strand=D; shift=9; score=38.8571; ---------TrATCRATaa ; cor=0.768; Ncor=0.698; logoDP=8.936; NIcor=0.681; NsEucl=0.890; SSD=2.407; NSW=0.880; rcor=61; rNcor=3; rlogoDP=13; rNIcor=4; rNsEucl=50; rSSD=80; rNSW=61; rank_mean=38.857; match_rank=32 a 0 0 0 0 0 0 0 0 0 8111 45569 45569 479 74 13767 45569 396 45569 19809 c 0 0 0 0 0 0 0 0 0 4573 5067 250 1841 45569 208 69 278 11730 9534 g 0 0 0 0 0 0 0 0 0 4247 23534 540 485 94 31803 163 66 7587 5056 t 0 0 0 0 0 0 0 0 0 45569 12191 345 45569 736 395 191 45569 12097 11171
5195_CUX1_DBD_1_HumanTF_1.0__shift0 (5195_CUX1_DBD_1_HumanTF_1.0_)		0.854	0.405	7.521	0.397	0.905	1.447	0.920	23	87	29	55	27	32	26	39.857	38	; oligos_6nt_mkv2 versus 5195_CUX1_DBD_1_HumanTF_1.0_; m=15/35; ncol2=17; w=9; offset=-8; strand=D; shift=0; score=39.8571; ATCrATmmstrATCrAT-- ; cor=0.854; Ncor=0.405; logoDP=7.521; NIcor=0.397; NsEucl=0.905; SSD=1.447; NSW=0.920; rcor=23; rNcor=87; rlogoDP=29; rNIcor=55; rNsEucl=27; rSSD=32; rNSW=26; rank_mean=39.857; match_rank=38 a 18540 327 448 5977 18540 1598 7788 7150 4224 3402 6466 18540 245 353 7775 18540 1425 0 0 c 217 549 18540 268 196 565 4732 5224 6088 3307 1417 217 338 18540 308 198 414 0 0 g 645 252 307 12562 221 195 2182 3370 4885 3606 6842 639 184 235 10764 246 165 0 0 t 948 18540 1083 219 332 18540 3837 2796 3344 8224 3814 793 18540 371 196 478 18540 0 0
1000_UP00185_UniPROBE_20120919__shift5 (1000_UP00185_UniPROBE_20120919_)		0.780	0.505	6.380	0.516	0.904	2.227	0.899	52	32	43	19	33	72	48	42.714	40	; oligos_6nt_mkv2 versus 1000_UP00185_UniPROBE_20120919_; m=16/35; ncol2=17; w=11; offset=-3; strand=D; shift=5; score=42.7143; -----yyaymCATCAAwmw ; cor=0.780; Ncor=0.505; logoDP=6.380; NIcor=0.516; NsEucl=0.904; SSD=2.227; NSW=0.899; rcor=52; rNcor=32; rlogoDP=43; rNIcor=19; rNsEucl=33; rSSD=72; rNSW=48; rank_mean=42.714; match_rank=40 a 0 0 0 0 0 21 6 59 12 37 11 86 3 3 93 74 31 32 39 c 0 0 0 0 0 28 50 4 40 39 73 2 1 95 3 6 5 32 14 g 0 0 0 0 0 15 15 14 9 11 9 7 1 1 2 3 6 15 9 t 0 0 0 0 0 36 29 23 39 13 7 5 95 1 2 17 58 21 38
2984_PH0134.1_JASPAR_CORE_2009__shift5 (2984_PH0134.1_JASPAR_CORE_2009_)		0.780	0.505	6.380	0.516	0.904	2.227	0.899	52	32	43	19	33	72	48	42.714	41	; oligos_6nt_mkv2 versus 2984_PH0134.1_JASPAR_CORE_2009_; m=17/35; ncol2=17; w=11; offset=-3; strand=D; shift=5; score=42.7143; -----yyaymCATCAAwmw ; cor=0.780; Ncor=0.505; logoDP=6.380; NIcor=0.516; NsEucl=0.904; SSD=2.227; NSW=0.899; rcor=52; rNcor=32; rlogoDP=43; rNIcor=19; rNsEucl=33; rSSD=72; rNSW=48; rank_mean=42.714; match_rank=41 a 0 0 0 0 0 21 6 59 12 37 11 86 3 3 93 74 31 32 39 c 0 0 0 0 0 28 49 3 40 39 73 2 1 95 3 6 5 32 14 g 0 0 0 0 0 15 15 14 9 11 9 7 1 1 2 3 6 15 9 t 0 0 0 0 0 36 29 23 39 13 7 5 95 1 2 17 58 21 38
2329_CN0166.1_JASPAR_CORE_2009__shift2 (2329_CN0166.1_JASPAR_CORE_2009_)		0.850	0.400	8.262	0.376	0.894	1.446	0.910	24	88	19	58	46	31	33	42.714	42	; oligos_6nt_mkv2 versus 2329_CN0166.1_JASPAR_CORE_2009_; m=18/35; ncol2=14; w=8; offset=-6; strand=D; shift=2; score=42.7143; --CATGCTGAGATCAA--- ; cor=0.850; Ncor=0.400; logoDP=8.262; NIcor=0.376; NsEucl=0.894; SSD=1.446; NSW=0.910; rcor=24; rNcor=88; rlogoDP=19; rNIcor=58; rNsEucl=46; rSSD=31; rNSW=33; rank_mean=42.714; match_rank=42 a 0 0 2 42 2 2 0 0 0 48 1 41 2 3 49 47 0 0 0 c 0 0 46 5 0 1 49 0 0 0 0 5 2 40 0 0 0 0 0 g 0 0 0 0 1 45 0 0 49 1 48 0 2 6 0 0 0 0 0 t 0 0 1 2 46 1 0 49 0 0 0 3 43 0 0 2 0 0 0
7440_HNF6_f1_HOCOMOCO_v9__rc_shift6 (7440_HNF6_f1_HOCOMOCO_v9__rc)		0.805	0.681	0.872	-0.173	0.907	2.093	0.905	38	5	76	86	23	55	36	45.571	45	; oligos_6nt_mkv2 versus 7440_HNF6_f1_HOCOMOCO_v9__rc; m=19/35; ncol2=13; w=11; offset=-2; strand=R; shift=6; score=45.5714; ------whwaARTCAATAw ; cor=0.805; Ncor=0.681; logoDP=0.872; NIcor=-0.173; NsEucl=0.907; SSD=2.093; NSW=0.905; rcor=38; rNcor=5; rlogoDP=76; rNIcor=86; rNsEucl=23; rSSD=55; rNSW=36; rank_mean=45.571; match_rank=45 a 0 0 0 0 0 0 9 9 11 16 19 17 0 0 20 24 0 17 13 c 0 0 0 0 0 0 3 7 2 0 2 0 1 24 3 0 0 1 0 g 0 0 0 0 0 0 5 2 3 3 1 7 0 0 1 0 0 4 4 t 0 0 0 0 0 0 7 6 8 5 2 0 23 0 0 0 24 2 7
6138_1j5n_A_3D-footprint_20130124__shift11 (6138_1j5n_A_3D-footprint_20130124_)		0.773	0.492	9.628	0.518	0.855	2.048	0.854	58	35	9	18	77	52	75	46.286	47	; oligos_6nt_mkv2 versus 6138_1j5n_A_3D-footprint_20130124_; m=20/35; ncol2=7; w=7; offset=3; strand=D; shift=11; score=46.2857; -----------AACAATc- ; cor=0.773; Ncor=0.492; logoDP=9.628; NIcor=0.518; NsEucl=0.855; SSD=2.048; NSW=0.854; rcor=58; rNcor=35; rlogoDP=9; rNIcor=18; rNsEucl=77; rSSD=52; rNSW=75; rank_mean=46.286; match_rank=47 a 0 0 0 0 0 0 0 0 0 0 0 96 76 0 96 96 0 19 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 96 0 0 0 38 0 g 0 0 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 19 0 t 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 96 20 0
7627_SOX10_si_HOCOMOCO_v9__shift13 (7627_SOX10_si_HOCOMOCO_v9_)		0.801	0.437	5.845	0.418	0.867	1.269	0.894	42	54	48	43	70	21	51	47.000	49	; oligos_6nt_mkv2 versus 7627_SOX10_si_HOCOMOCO_v9_; m=21/35; ncol2=6; w=6; offset=5; strand=D; shift=13; score= 47; -------------CAAwGr ; cor=0.801; Ncor=0.437; logoDP=5.845; NIcor=0.418; NsEucl=0.867; SSD=1.269; NSW=0.894; rcor=42; rNcor=54; rlogoDP=48; rNIcor=43; rNsEucl=70; rSSD=21; rNSW=51; rank_mean=47.000; match_rank=49 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 31 15 2 13 c 0 0 0 0 0 0 0 0 0 0 0 0 0 31 0 0 0 0 7 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 29 10 t 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 14 1 2
3061_FNR_RegulonDB_7.5__rc_shift2 (3061_FNR_RegulonDB_7.5__rc)		0.863	0.406	6.281	0.405	0.889	1.568	0.902	19	85	47	54	52	35	39	47.286	50	; oligos_6nt_mkv2 versus 3061_FNR_RegulonDB_7.5__rc; m=22/35; ncol2=14; w=8; offset=-6; strand=R; shift=2; score=47.2857; --TTGATrtwrAtCAa--- ; cor=0.863; Ncor=0.406; logoDP=6.281; NIcor=0.405; NsEucl=0.889; SSD=1.568; NSW=0.902; rcor=19; rNcor=85; rlogoDP=47; rNIcor=54; rNsEucl=52; rSSD=35; rNSW=39; rank_mean=47.286; match_rank=50 a 0 0 2 2 6 79 6 29 12 29 35 57 14 2 64 48 0 0 0 c 0 0 0 0 5 0 11 11 11 16 3 13 8 58 6 10 0 0 0 g 0 0 8 1 72 0 0 23 12 10 28 3 14 10 8 8 0 0 0 t 0 0 73 80 0 4 66 20 48 28 17 10 47 13 5 17 0 0 0
3788_UP00091_UniPROBE_20120919__shift6 (3788_UP00091_UniPROBE_20120919_)		0.753	0.517	7.714	0.528	0.897	2.556	0.884	82	25	25	16	42	83	60	47.571	51	; oligos_6nt_mkv2 versus 3788_UP00091_UniPROBE_20120919_; m=23/35; ncol2=16; w=11; offset=-2; strand=D; shift=6; score=47.5714; ------wwdrgAACAATwa ; cor=0.753; Ncor=0.517; logoDP=7.714; NIcor=0.528; NsEucl=0.897; SSD=2.556; NSW=0.884; rcor=82; rNcor=25; rlogoDP=25; rNIcor=16; rNsEucl=42; rSSD=83; rNSW=60; rank_mean=47.571; match_rank=51 a 0 0 0 0 0 0 31 26 26 45 15 83 0.98 1 0.97 0.97 0.03 49 45 c 0 0 0 0 0 0 13 20 12 9 9 3 0 93 0 0 0.01 2 10 g 0 0 0 0 0 0 17 14 26 29 63 13 0.01 1 0.01 0.01 0 8 24 t 0 0 0 0 0 0 39 40 36 17 13 1 0.01 5 0.02 0.01 0.95 41 21
2682_PB0072.1_JASPAR_CORE_2009__shift6 (2682_PB0072.1_JASPAR_CORE_2009_)		0.753	0.517	7.665	0.527	0.897	2.555	0.884	83	26	28	17	41	82	59	48.000	54	; oligos_6nt_mkv2 versus 2682_PB0072.1_JASPAR_CORE_2009_; m=24/35; ncol2=16; w=11; offset=-2; strand=D; shift=6; score= 48; ------wwdrgAACAATwa ; cor=0.753; Ncor=0.517; logoDP=7.665; NIcor=0.527; NsEucl=0.897; SSD=2.555; NSW=0.884; rcor=83; rNcor=26; rlogoDP=28; rNIcor=17; rNsEucl=41; rSSD=82; rNSW=59; rank_mean=48.000; match_rank=54 a 0 0 0 0 0 0 31 26 26 45 15 83 98 1 97 97 3 49 45 c 0 0 0 0 0 0 13 20 12 9 9 3 0 94 0 0 1 2 10 g 0 0 0 0 0 0 17 15 26 29 63 13 1 1 1 1 0 9 24 t 0 0 0 0 0 0 39 40 36 17 13 2 1 5 2 1 95 41 20
6753_6gat_A_3D-footprint_20130124__shift9 (6753_6gat_A_3D-footprint_20130124_)		0.803	0.438	4.707	0.416	0.863	1.346	0.888	40	53	58	44	72	25	54	49.429	56	; oligos_6nt_mkv2 versus 6753_6gat_A_3D-footprint_20130124_; m=25/35; ncol2=6; w=6; offset=1; strand=D; shift=9; score=49.4286; ---------CnATCA---- ; cor=0.803; Ncor=0.438; logoDP=4.707; NIcor=0.416; NsEucl=0.863; SSD=1.346; NSW=0.888; rcor=40; rNcor=53; rlogoDP=58; rNIcor=44; rNsEucl=72; rSSD=25; rNSW=54; rank_mean=49.429; match_rank=56 a 0 0 0 0 0 0 0 0 0 11 24 67 9 0 96 0 0 0 0 c 0 0 0 0 0 0 0 0 0 67 24 9 11 96 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 9 24 11 9 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 9 24 9 67 0 0 0 0 0 0
7634_SOX5_f1_HOCOMOCO_v9__shift11 (7634_SOX5_f1_HOCOMOCO_v9_)		0.767	0.488	6.350	0.491	0.857	2.004	0.857	62	37	45	22	76	47	74	51.857	61	; oligos_6nt_mkv2 versus 7634_SOX5_f1_HOCOMOCO_v9_; m=26/35; ncol2=7; w=7; offset=3; strand=D; shift=11; score=51.8571; -----------AACAATr- ; cor=0.767; Ncor=0.488; logoDP=6.350; NIcor=0.491; NsEucl=0.857; SSD=2.004; NSW=0.857; rcor=62; rNcor=37; rlogoDP=45; rNIcor=22; rNsEucl=76; rSSD=47; rNSW=74; rank_mean=51.857; match_rank=61 a 0 0 0 0 0 0 0 0 0 0 0 61 64 2 67 62 5 27 0 c 0 0 0 0 0 0 0 0 0 0 0 1 0 62 0 5 4 11 0 g 0 0 0 0 0 0 0 0 0 0 0 3 4 2 1 2 0 22 0 t 0 0 0 0 0 0 0 0 0 0 0 4 1 3 1 0 60 9 0
1741_MA0182.1_JASPAR_CORE_2009__rc_shift13 (1741_MA0182.1_JASPAR_CORE_2009__rc)		0.826	0.413	0.779	-0.103	0.877	1.096	0.909	30	76	78	76	62	15	34	53.000	62	; oligos_6nt_mkv2 versus 1741_MA0182.1_JASPAR_CORE_2009__rc; m=27/35; ncol2=7; w=6; offset=5; strand=R; shift=13; score= 53; -------------yAATwA ; cor=0.826; Ncor=0.413; logoDP=0.779; NIcor=-0.103; NsEucl=0.877; SSD=1.096; NSW=0.909; rcor=30; rNcor=76; rlogoDP=78; rNIcor=76; rNsEucl=62; rSSD=15; rNSW=34; rank_mean=53.000; match_rank=62 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 30 0 17 22 c 0 0 0 0 0 0 0 0 0 0 0 0 0 15 6 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 30 13 7
2872_PH0014.1_JASPAR_CORE_2009__shift3 (2872_PH0014.1_JASPAR_CORE_2009_)		0.761	0.428	6.819	0.429	0.882	2.237	0.876	73	58	37	37	55	74	63	56.714	66	; oligos_6nt_mkv2 versus 2872_PH0014.1_JASPAR_CORE_2009_; m=28/35; ncol2=14; w=9; offset=-5; strand=D; shift=3; score=56.7143; ---rTGATssmATCAaw-- ; cor=0.761; Ncor=0.428; logoDP=6.819; NIcor=0.429; NsEucl=0.882; SSD=2.237; NSW=0.876; rcor=73; rNcor=58; rlogoDP=37; rNIcor=37; rNsEucl=55; rSSD=74; rNSW=63; rank_mean=56.714; match_rank=66 a 0 0 0 34 3 4 98 4 10 22 54 95 1 0 95 61 36 0 0 c 0 0 0 18 0 2 1 0 37 28 34 3 1 97 1 14 21 0 0 g 0 0 0 26 0 93 1 6 29 35 8 1 0 0 1 15 10 0 0 t 0 0 0 22 96 1 1 90 24 15 4 1 99 2 3 10 33 0 0
3893_UP00198_UniPROBE_20120919__shift3 (3893_UP00198_UniPROBE_20120919_)		0.761	0.428	6.819	0.429	0.882	2.237	0.876	73	58	37	37	55	74	63	56.714	67	; oligos_6nt_mkv2 versus 3893_UP00198_UniPROBE_20120919_; m=29/35; ncol2=14; w=9; offset=-5; strand=D; shift=3; score=56.7143; ---rTGATssmATCAaw-- ; cor=0.761; Ncor=0.428; logoDP=6.819; NIcor=0.429; NsEucl=0.882; SSD=2.237; NSW=0.876; rcor=73; rNcor=58; rlogoDP=37; rNIcor=37; rNsEucl=55; rSSD=74; rNSW=63; rank_mean=56.714; match_rank=67 a 0 0 0 34 0.03 4 98 0.04 10 22 54 95 0.01 0 95 61 36 0 0 c 0 0 0 18 0 2 1 0 37 28 34 3 0.01 0.97 1 14 21 0 0 g 0 0 0 26 0 93 1 0.06 29 35 8 1 0 0 1 15 10 0 0 t 0 0 0 22 0.96 1 0 0.90 24 15 4 1 0.99 0.02 3 10 33 0 0
2619_MA0389.1_JASPAR_CORE_2009__rc_shift7 (2619_MA0389.1_JASPAR_CORE_2009__rc)		0.771	0.450	0.785	-0.004	0.872	1.616	0.885	60	51	77	70	68	37	57	60.000	73	; oligos_6nt_mkv2 versus 2619_MA0389.1_JASPAR_CORE_2009__rc; m=30/35; ncol2=8; w=7; offset=-1; strand=R; shift=7; score= 60; -------gkAGATCt---- ; cor=0.771; Ncor=0.450; logoDP=0.785; NIcor=-0.004; NsEucl=0.872; SSD=1.616; NSW=0.885; rcor=60; rNcor=51; rlogoDP=77; rNIcor=70; rNsEucl=68; rSSD=37; rNSW=57; rank_mean=60.000; match_rank=73 a 0 0 0 0 0 0 0 16 11 74 0 85 3 2 6 0 0 0 0 c 0 0 0 0 0 0 0 18 13 3 0 2 0 90 19 0 0 0 0 g 0 0 0 0 0 0 0 42 30 19 99 0 0 2 9 0 0 0 0 t 0 0 0 0 0 0 0 24 46 4 0 13 97 6 66 0 0 0 0
7604_RARG_f1_HOCOMOCO_v9__shift9 (7604_RARG_f1_HOCOMOCO_v9_)		0.752	0.410	7.248	0.429	0.840	1.845	0.846	84	79	32	36	82	41	81	62.143	77	; oligos_6nt_mkv2 versus 7604_RARG_f1_HOCOMOCO_v9_; m=31/35; ncol2=6; w=6; offset=1; strand=D; shift=9; score=62.1429; ---------AGKTCA---- ; cor=0.752; Ncor=0.410; logoDP=7.248; NIcor=0.429; NsEucl=0.840; SSD=1.845; NSW=0.846; rcor=84; rNcor=79; rlogoDP=32; rNIcor=36; rNsEucl=82; rSSD=41; rNSW=81; rank_mean=62.143; match_rank=77 a 0 0 0 0 0 0 0 0 0 23 0 0 0 0 27 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 29 2 0 0 0 0 g 0 0 0 0 0 0 0 0 0 6 29 21 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 8 29 0 0 0 0 0 0
2559_MA0301.1_JASPAR_CORE_2009__rc_shift6 (2559_MA0301.1_JASPAR_CORE_2009__rc)		0.776	0.418	0.126	-0.106	0.874	1.545	0.890	56	69	85	77	64	34	53	62.571	78	; oligos_6nt_mkv2 versus 2559_MA0301.1_JASPAR_CORE_2009__rc; m=32/35; ncol2=9; w=7; offset=-2; strand=R; shift=6; score=62.5714; ------kktrGATCt---- ; cor=0.776; Ncor=0.418; logoDP=0.126; NIcor=-0.106; NsEucl=0.874; SSD=1.545; NSW=0.890; rcor=56; rNcor=69; rlogoDP=85; rNIcor=77; rNsEucl=64; rSSD=34; rNSW=53; rank_mean=62.571; match_rank=78 a 0 0 0 0 0 0 21 17 12 63 2 87 8 1 6 0 0 0 0 c 0 0 0 0 0 0 21 21 18 4 1 1 0 88 20 0 0 0 0 g 0 0 0 0 0 0 25 33 19 27 94 0 0 2 9 0 0 0 0 t 0 0 0 0 0 0 32 28 51 6 3 12 92 8 65 0 0 0 0
2526_MA0151.1_JASPAR_CORE_2009__shift11 (2526_MA0151.1_JASPAR_CORE_2009_)		0.758	0.414	8.186	0.386	0.833	1.997	0.834	78	75	20	57	84	45	84	63.286	80	; oligos_6nt_mkv2 versus 2526_MA0151.1_JASPAR_CORE_2009_; m=33/35; ncol2=6; w=6; offset=3; strand=D; shift=11; score=63.2857; -----------ATyAAA-- ; cor=0.758; Ncor=0.414; logoDP=8.186; NIcor=0.386; NsEucl=0.833; SSD=1.997; NSW=0.834; rcor=78; rNcor=75; rlogoDP=20; rNIcor=57; rNsEucl=84; rSSD=45; rNSW=84; rank_mean=63.286; match_rank=80 a 0 0 0 0 0 0 0 0 0 0 0 27 0 1 27 27 20 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 27 17 0 0 6 0 0
1793_MA0235.1_JASPAR_CORE_2009__rc_shift9 (1793_MA0235.1_JASPAR_CORE_2009__rc)		0.759	0.483	0.148	-0.170	0.853	2.124	0.848	76	41	82	85	79	60	78	71.571	86	; oligos_6nt_mkv2 versus 1793_MA0235.1_JASPAR_CORE_2009__rc; m=34/35; ncol2=7; w=7; offset=1; strand=R; shift=9; score=71.5714; ---------hAATCAA--- ; cor=0.759; Ncor=0.483; logoDP=0.148; NIcor=-0.170; NsEucl=0.853; SSD=2.124; NSW=0.848; rcor=76; rNcor=41; rlogoDP=82; rNIcor=85; rNsEucl=79; rSSD=60; rNSW=78; rank_mean=71.571; match_rank=86 a 0 0 0 0 0 0 0 0 0 6 15 15 0 0 15 12 0 0 0 c 0 0 0 0 0 0 0 0 0 4 0 0 0 15 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 t 0 0 0 0 0 0 0 0 0 5 0 0 15 0 0 1 0 0 0
2670_MF0011.1_JASPAR_CORE_2009__rc_shift11 (2670_MF0011.1_JASPAR_CORE_2009__rc)		0.751	0.410	1.677	0.106	0.834	1.984	0.835	85	80	71	60	83	44	83	72.286	88	; oligos_6nt_mkv2 versus 2670_MF0011.1_JASPAR_CORE_2009__rc; m=35/35; ncol2=6; w=6; offset=3; strand=R; shift=11; score=72.2857; -----------aACAAw-- ; cor=0.751; Ncor=0.410; logoDP=1.677; NIcor=0.106; NsEucl=0.834; SSD=1.984; NSW=0.835; rcor=85; rNcor=80; rlogoDP=71; rNIcor=60; rNsEucl=83; rSSD=44; rNSW=83; rank_mean=72.286; match_rank=88 a 0 0 0 0 0 0 0 0 0 0 0 61.71 76.2 7.53 92.51 77.94 30.58 0 0 c 0 0 0 0 0 0 0 0 0 0 0 10.7 3.14 74.53 0.92 14.03 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 17.54 8.38 6.65 4.96 6.34 9 0 0 t 0 0 0 0 0 0 0 0 0 0 0 10.05 12.28 11.29 1.61 1.68 60.43 0 0

One-to-n matrix alignment; reference matrix: dyads_m3_shift7 ; 34 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_shift7 (dyads_m3)																		; dyads_m3; m=0 (reference); ncol1=11; shift=7; ncol=21; -------ymGATCAAAtw--- ; Alignment reference a 0 0 0 0 0 0 0 2 6 0 11 0 0 11 11 11 2 4 0 0 0 c 0 0 0 0 0 0 0 3 3 0 0 0 11 0 0 0 2 1 0 0 0 g 0 0 0 0 0 0 0 2 0 11 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 4 2 0 0 11 0 0 0 0 7 6 0 0 0
2526_MA0151.1_JASPAR_CORE_2009__shift10 (2526_MA0151.1_JASPAR_CORE_2009_)		0.887	0.484	8.694	0.469	0.885	0.960	0.920	13	39	15	26	54	12	25	26.286	9	; dyads_m3 versus 2526_MA0151.1_JASPAR_CORE_2009_; m=1/33; ncol2=6; w=6; offset=3; strand=D; shift=10; score=26.2857; ----------ATyAAA----- ; cor=0.887; Ncor=0.484; logoDP=8.694; NIcor=0.469; NsEucl=0.885; SSD=0.960; NSW=0.920; rcor=13; rNcor=39; rlogoDP=15; rNIcor=26; rNsEucl=54; rSSD=12; rNSW=25; rank_mean=26.286; match_rank=9 a 0 0 0 0 0 0 0 0 0 0 27 0 1 27 27 20 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 27 17 0 0 6 0 0 0 0 0
6733_4euw_A_3D-footprint_20130124__shift11 (6733_4euw_A_3D-footprint_20130124_)		0.883	0.481	7.280	0.491	0.890	0.877	0.927	16	42	31	23	51	10	18	27.286	13	; dyads_m3 versus 6733_4euw_A_3D-footprint_20130124_; m=2/33; ncol2=6; w=6; offset=4; strand=D; shift=11; score=27.2857; -----------TcAAAg---- ; cor=0.883; Ncor=0.481; logoDP=7.280; NIcor=0.491; NsEucl=0.890; SSD=0.877; NSW=0.927; rcor=16; rNcor=42; rlogoDP=31; rNIcor=23; rNsEucl=51; rSSD=10; rNSW=18; rank_mean=27.286; match_rank=13 a 0 0 0 0 0 0 0 0 0 0 0 0 12 96 84 96 12 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 60 0 0 0 12 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 12 0 12 0 60 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 96 12 0 0 0 12 0 0 0 0
5048_ZmHOX2a_2__Athamap_20091028__rc_shift7 (5048_ZmHOX2a_2__Athamap_20091028__rc)		0.940	0.598	0.123	-0.161	0.932	0.456	0.967	3	10	86	84	3	3	3	27.429	14	; dyads_m3 versus 5048_ZmHOX2a_2__Athamap_20091028__rc; m=3/33; ncol2=7; w=7; offset=0; strand=R; shift=7; score=27.4286; -------cmGATCa------- ; cor=0.940; Ncor=0.598; logoDP=0.123; NIcor=-0.161; NsEucl=0.932; SSD=0.456; NSW=0.967; rcor=3; rNcor=10; rlogoDP=86; rNIcor=84; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=27.429; match_rank=14 a 0 0 0 0 0 0 0 6 16 0 27 0 0 15 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 14 7 0 0 0 27 5 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 4 4 27 0 0 0 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 3 0 0 0 27 0 5 0 0 0 0 0 0 0
2653_MA0434.1_JASPAR_CORE_2009__shift5 (2653_MA0434.1_JASPAR_CORE_2009_)		0.862	0.464	6.479	0.443	0.898	1.014	0.928	21	47	40	27	40	13	17	29.286	16	; dyads_m3 versus 2653_MA0434.1_JASPAR_CORE_2009_; m=4/33; ncol2=9; w=7; offset=-2; strand=D; shift=5; score=29.2857; -----yGymrATCm------- ; cor=0.862; Ncor=0.464; logoDP=6.479; NIcor=0.443; NsEucl=0.898; SSD=1.014; NSW=0.928; rcor=21; rNcor=47; rlogoDP=40; rNIcor=27; rNsEucl=40; rSSD=13; rNSW=17; rank_mean=29.286; match_rank=16 a 0 0 0 0 0 11 0 9 63 40 100 0 0 36 0 0 0 0 0 0 0 c 0 0 0 0 0 36 0 26 26 0 0 0 100 30 0 0 0 0 0 0 0 g 0 0 0 0 0 11 100 0 0 60 0 0 0 17 0 0 0 0 0 0 0 t 0 0 0 0 0 41 0 65 11 0 0 100 0 17 0 0 0 0 0 0 0
1939_PB0082.1_JASPAR_CORE_2009__shift5 (1939_PB0082.1_JASPAR_CORE_2009_)		0.799	0.517	8.434	0.552	0.906	2.134	0.903	43	27	17	13	24	62	37	31.857	20	; dyads_m3 versus 1939_PB0082.1_JASPAR_CORE_2009_; m=5/33; ncol2=17; w=11; offset=-2; strand=D; shift=5; score=31.8571; -----twwasATCAAAGgrww ; cor=0.799; Ncor=0.517; logoDP=8.434; NIcor=0.552; NsEucl=0.906; SSD=2.134; NSW=0.903; rcor=43; rNcor=27; rlogoDP=17; rNIcor=13; rNsEucl=24; rSSD=62; rNSW=37; rank_mean=31.857; match_rank=20 a 0 0 0 0 0 19 37 25 58 4 76 6 4 96 97 94 13 21 49 40 31 c 0 0 0 0 0 20 23 17 4 40 1 1 87 0 0 0 6 17 13 20 23 g 0 0 0 0 0 18 12 13 13 50 1 0 6 0 1 2 80 48 31 15 16 t 0 0 0 0 0 43 27 45 24 7 23 93 3 3 1 4 2 13 8 25 30
7482_LEF1_f1_HOCOMOCO_v9__rc_shift10 (7482_LEF1_f1_HOCOMOCO_v9__rc)		0.917	0.500	2.545	0.028	0.900	0.726	0.939	8	34	67	68	38	6	13	33.429	23	; dyads_m3 versus 7482_LEF1_f1_HOCOMOCO_v9__rc; m=6/33; ncol2=6; w=6; offset=3; strand=R; shift=10; score=33.4286; ----------wwCAAA----- ; cor=0.917; Ncor=0.500; logoDP=2.545; NIcor=0.028; NsEucl=0.900; SSD=0.726; NSW=0.939; rcor=8; rNcor=34; rlogoDP=67; rNIcor=68; rNsEucl=38; rSSD=6; rNSW=13; rank_mean=33.429; match_rank=23 a 0 0 0 0 0 0 0 0 0 0 38 28 0 67 67 65 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 3 0 67 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2 4 0 0 0 1 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 24 35 0 0 0 1 0 0 0 0 0
6387_2a07_K_3D-footprint_20130124__rc_shift12 (6387_2a07_K_3D-footprint_20130124__rc)		0.958	0.436	0.093	-0.128	0.925	0.282	0.972	1	55	88	80	11	1	1	33.857	24	; dyads_m3 versus 6387_2a07_K_3D-footprint_20130124__rc; m=7/33; ncol2=5; w=5; offset=5; strand=R; shift=12; score=33.8571; ------------CAAat---- ; cor=0.958; Ncor=0.436; logoDP=0.093; NIcor=-0.128; NsEucl=0.925; SSD=0.282; NSW=0.972; rcor=1; rNcor=55; rlogoDP=88; rNIcor=80; rNsEucl=11; rSSD=1; rNSW=1; rank_mean=33.857; match_rank=24 a 0 0 0 0 0 0 0 0 0 0 0 0 0 96 96 54 13 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 96 0 0 13 16 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 13 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 54 0 0 0 0
3755_UP00058_UniPROBE_20120919__shift5 (3755_UP00058_UniPROBE_20120919_)		0.796	0.515	8.422	0.550	0.905	2.165	0.902	44	28	18	14	28	66	41	34.143	25	; dyads_m3 versus 3755_UP00058_UniPROBE_20120919_; m=8/33; ncol2=17; w=11; offset=-2; strand=D; shift=5; score=34.1429; -----twwwsATCAAAGgrww ; cor=0.796; Ncor=0.515; logoDP=8.422; NIcor=0.550; NsEucl=0.905; SSD=2.165; NSW=0.902; rcor=44; rNcor=28; rlogoDP=18; rNIcor=14; rNsEucl=28; rSSD=66; rNSW=41; rank_mean=34.143; match_rank=25 a 0 0 0 0 0 19 37 25 58 4 75 0.06 4 0.96 0.97 0.94 12 21 49 40 31 c 0 0 0 0 0 20 23 17 4 40 1 0.01 87 0 0 0 6 17 13 20 23 g 0 0 0 0 0 18 13 13 13 49 1 0 6 0 0.01 0.02 80 49 31 15 16 t 0 0 0 0 0 43 27 45 25 7 23 0.93 3 0.03 0.01 0.04 2 13 7 25 30
1940_PB0083.1_JASPAR_CORE_2009__shift5 (1940_PB0083.1_JASPAR_CORE_2009_)		0.795	0.515	7.733	0.554	0.906	2.161	0.902	45	29	24	11	26	65	40	34.286	26	; dyads_m3 versus 1940_PB0083.1_JASPAR_CORE_2009_; m=9/33; ncol2=17; w=11; offset=-2; strand=D; shift=5; score=34.2857; -----twwasWTCAAAGgrah ; cor=0.795; Ncor=0.515; logoDP=7.733; NIcor=0.554; NsEucl=0.906; SSD=2.161; NSW=0.902; rcor=45; rNcor=29; rlogoDP=24; rNIcor=11; rNsEucl=26; rSSD=65; rNSW=40; rank_mean=34.286; match_rank=26 a 0 0 0 0 0 17 34 30 60 4 73 7 5 96 96 94 16 23 56 49 31 c 0 0 0 0 0 20 23 17 5 38 1 1 82 1 0 1 6 15 12 21 25 g 0 0 0 0 0 22 14 14 13 53 1 0 10 1 2 2 76 52 25 12 13 t 0 0 0 0 0 41 29 38 21 5 26 92 4 3 2 4 2 9 6 17 31
3751_UP00054_UniPROBE_20120919__shift5 (3751_UP00054_UniPROBE_20120919_)		0.795	0.514	7.843	0.554	0.905	2.167	0.901	46	30	22	12	29	67	42	35.429	27	; dyads_m3 versus 3751_UP00054_UniPROBE_20120919_; m=10/33; ncol2=17; w=11; offset=-2; strand=D; shift=5; score=35.4286; -----twwasWTCAAAGgrah ; cor=0.795; Ncor=0.514; logoDP=7.843; NIcor=0.554; NsEucl=0.905; SSD=2.167; NSW=0.901; rcor=46; rNcor=30; rlogoDP=22; rNIcor=12; rNsEucl=29; rSSD=67; rNSW=42; rank_mean=35.429; match_rank=27 a 0 0 0 0 0 17 34 30 60 4 72 0.07 4 96 0.96 93 16 23 56 49 31 c 0 0 0 0 0 20 23 17 5 38 1 0.01 82 1 0 1 6 15 13 22 25 g 0 0 0 0 0 22 14 14 14 53 1 0 10 0 0.02 2 76 53 25 12 13 t 0 0 0 0 0 41 29 39 21 5 26 0.92 4 3 0.02 4 2 9 6 17 31
1795_MA0237.1_JASPAR_CORE_2009__rc_shift9 (1795_MA0237.1_JASPAR_CORE_2009__rc)		0.888	0.646	2.118	0.068	0.897	1.360	0.915	12	8	68	66	43	26	30	36.143	28	; dyads_m3 versus 1795_MA0237.1_JASPAR_CORE_2009__rc; m=11/33; ncol2=8; w=8; offset=2; strand=R; shift=9; score=36.1429; ---------kWTCAAAr---- ; cor=0.888; Ncor=0.646; logoDP=2.118; NIcor=0.068; NsEucl=0.897; SSD=1.360; NSW=0.915; rcor=12; rNcor=8; rlogoDP=68; rNIcor=66; rNsEucl=43; rSSD=26; rNSW=30; rank_mean=36.143; match_rank=28 a 0 0 0 0 0 0 0 0 0 4 17 3 3 23 22 20 8 0 0 0 0 c 0 0 0 0 0 0 0 0 0 3 0 5 20 0 1 0 3 0 0 0 0 g 0 0 0 0 0 0 0 0 0 11 0 0 2 0 0 3 10 0 0 0 0 t 0 0 0 0 0 0 0 0 0 7 8 17 0 2 2 2 4 0 0 0 0
2329_CN0166.1_JASPAR_CORE_2009__shift1 (2329_CN0166.1_JASPAR_CORE_2009_)		0.864	0.407	8.500	0.387	0.898	1.323	0.917	18	84	16	56	39	22	29	37.714	29	; dyads_m3 versus 2329_CN0166.1_JASPAR_CORE_2009_; m=12/33; ncol2=14; w=8; offset=-6; strand=D; shift=1; score=37.7143; -CATGCTGAGATCAA------ ; cor=0.864; Ncor=0.407; logoDP=8.500; NIcor=0.387; NsEucl=0.898; SSD=1.323; NSW=0.917; rcor=18; rNcor=84; rlogoDP=16; rNIcor=56; rNsEucl=39; rSSD=22; rNSW=29; rank_mean=37.714; match_rank=29 a 0 2 42 2 2 0 0 0 48 1 41 2 3 49 47 0 0 0 0 0 0 c 0 46 5 0 1 49 0 0 0 0 5 2 40 0 0 0 0 0 0 0 0 g 0 0 0 1 45 0 0 49 1 48 0 2 6 0 0 0 0 0 0 0 0 t 0 1 2 46 1 0 49 0 0 0 3 43 0 0 2 0 0 0 0 0 0
5494_LEF1_DBD_HumanTF_1.0__shift6 (5494_LEF1_DBD_HumanTF_1.0_)		0.777	0.570	11.529	0.608	0.894	2.736	0.876	55	14	1	7	47	84	65	39.000	33	; dyads_m3 versus 5494_LEF1_DBD_HumanTF_1.0_; m=13/33; ncol2=15; w=11; offset=-1; strand=D; shift=6; score= 39; ------aAAGATCAAAGgrww ; cor=0.777; Ncor=0.570; logoDP=11.529; NIcor=0.608; NsEucl=0.894; SSD=2.736; NSW=0.876; rcor=55; rNcor=14; rlogoDP=1; rNIcor=7; rNsEucl=47; rSSD=84; rNSW=65; rank_mean=39.000; match_rank=33 a 0 0 0 0 0 0 601 655 697 5 699 9 14 711 709 712 33 197 309 367 366 c 0 0 0 0 0 0 139 26 7 242 0 3 935 0 0 0 24 184 164 63 95 g 0 0 0 0 0 0 215 207 34 1053 4 0 49 0 4 13 1068 851 559 88 77 t 0 0 0 0 0 0 138 63 14 3 15 898 5 4 0 4 0 124 121 372 422
5900_Tcf7_DBD_HumanTF_1.0__shift6 (5900_Tcf7_DBD_HumanTF_1.0_)		0.766	0.702	11.009	0.742	0.891	2.849	0.870	64	2	2	1	49	86	71	39.286	34	; dyads_m3 versus 5900_Tcf7_DBD_HumanTF_1.0_; m=14/33; ncol2=12; w=11; offset=-1; strand=D; shift=6; score=39.2857; ------aAASATCAAAGg--- ; cor=0.766; Ncor=0.702; logoDP=11.009; NIcor=0.742; NsEucl=0.891; SSD=2.849; NSW=0.870; rcor=64; rNcor=2; rlogoDP=2; rNIcor=1; rNsEucl=49; rSSD=86; rNSW=71; rank_mean=39.286; match_rank=34 a 0 0 0 0 0 0 552 791 906 5 912 0 21 919 921 915 32 159 0 0 0 c 0 0 0 0 0 0 68 31 4 277 2 5 1018 0 6 0 0 146 0 0 0 g 0 0 0 0 0 0 117 144 27 744 4 18 28 5 10 0 846 600 0 0 0 t 0 0 0 0 0 0 97 111 31 6 42 874 21 6 3 4 0 89 0 0 0
3061_FNR_RegulonDB_7.5__shift1 (3061_FNR_RegulonDB_7.5_)		0.863	0.406	6.313	0.409	0.903	1.216	0.924	20	86	46	51	35	19	21	39.714	37	; dyads_m3 versus 3061_FNR_RegulonDB_7.5_; m=15/33; ncol2=14; w=8; offset=-6; strand=D; shift=1; score=39.7143; -tTGaTywayATCAA------ ; cor=0.863; Ncor=0.406; logoDP=6.313; NIcor=0.409; NsEucl=0.903; SSD=1.216; NSW=0.924; rcor=20; rNcor=86; rlogoDP=46; rNIcor=51; rNsEucl=35; rSSD=19; rNSW=21; rank_mean=39.714; match_rank=37 a 0 17 5 13 47 10 17 28 48 20 66 4 0 80 73 0 0 0 0 0 0 c 0 8 8 10 14 3 28 10 12 23 0 0 72 1 8 0 0 0 0 0 0 g 0 10 6 58 8 13 3 16 11 11 11 0 5 0 0 0 0 0 0 0 0 t 0 48 64 2 14 57 35 29 12 29 6 79 6 2 2 0 0 0 0 0 0
5863_TCF7L1_full_HumanTF_1.0__shift6 (5863_TCF7L1_full_HumanTF_1.0_)		0.750	0.688	10.294	0.720	0.888	3.015	0.863	87	4	5	2	53	88	72	44.429	43	; dyads_m3 versus 5863_TCF7L1_full_HumanTF_1.0_; m=16/33; ncol2=12; w=11; offset=-1; strand=D; shift=6; score=44.4286; ------AAAGATCAAAGG--- ; cor=0.750; Ncor=0.688; logoDP=10.294; NIcor=0.720; NsEucl=0.888; SSD=3.015; NSW=0.863; rcor=87; rNcor=4; rlogoDP=5; rNIcor=2; rNsEucl=53; rSSD=88; rNSW=72; rank_mean=44.429; match_rank=43 a 0 0 0 0 0 0 109 159 159 0 159 0 5 159 159 159 0 28 0 0 0 c 0 0 0 0 0 0 20 7 0 33 9 6 159 2 0 0 9 9 0 0 0 g 0 0 0 0 0 0 6 30 0 126 13 9 0 1 0 2 159 113 0 0 0 t 0 0 0 0 0 0 24 7 5 6 18 159 0 0 0 0 5 9 0 0 0
3780_UP00083_UniPROBE_20120919__rc_shift5 (3780_UP00083_UniPROBE_20120919__rc)		0.803	0.520	3.634	0.097	0.906	2.152	0.902	39	23	64	63	25	64	38	45.143	44	; dyads_m3 versus 3780_UP00083_UniPROBE_20120919__rc; m=17/33; ncol2=17; w=11; offset=-2; strand=R; shift=5; score=45.1429; -----tawasATCAAAGgrmh ; cor=0.803; Ncor=0.520; logoDP=3.634; NIcor=0.097; NsEucl=0.906; SSD=2.152; NSW=0.902; rcor=39; rNcor=23; rlogoDP=64; rNIcor=63; rNsEucl=25; rSSD=64; rNSW=38; rank_mean=45.143; match_rank=44 a 0 0 0 0 0 17 39 25 59 4 0.89 0.05 3 0.97 0.98 0.96 7 20 44 35 31 c 0 0 0 0 0 23 24 22 4 35 0 0 93 0 0 0 3 18 15 25 26 g 0 0 0 0 0 24 14 17 15 57 0 0 3 0 0.01 0.02 88 53 33 16 15 t 0 0 0 0 0 36 23 36 22 4 0.11 0.95 1 0.03 0.01 0.02 2 9 8 24 28
3764_UP00067_UniPROBE_20120919__rc_shift5 (3764_UP00067_UniPROBE_20120919__rc)		0.805	0.521	3.757	0.094	0.905	2.176	0.901	36	21	63	64	31	69	45	47.000	48	; dyads_m3 versus 3764_UP00067_UniPROBE_20120919__rc; m=18/33; ncol2=17; w=11; offset=-2; strand=R; shift=5; score= 47; -----kwwasATCAAAGgrwy ; cor=0.805; Ncor=0.521; logoDP=3.757; NIcor=0.094; NsEucl=0.905; SSD=2.176; NSW=0.901; rcor=36; rNcor=21; rlogoDP=63; rNIcor=64; rNsEucl=31; rSSD=69; rNSW=45; rank_mean=47.000; match_rank=48 a 0 0 0 0 0 19 40 26 62 2 0.92 0.03 2 0.97 0.99 0.97 5 17 38 32 22 c 0 0 0 0 0 22 17 22 6 28 0 0 95 0 0 0 4 14 14 24 30 g 0 0 0 0 0 34 15 17 12 67 0 0 3 0 0.01 0.02 90 62 40 15 15 t 0 0 0 0 0 25 28 35 20 3 0.08 0.97 0 0.02 0.01 0.02 1 7 8 29 33
2684_PB0084.1_JASPAR_CORE_2009__rc_shift5 (2684_PB0084.1_JASPAR_CORE_2009__rc)		0.801	0.518	3.622	0.097	0.905	2.175	0.901	41	24	65	62	30	68	44	47.714	52	; dyads_m3 versus 2684_PB0084.1_JASPAR_CORE_2009__rc; m=19/33; ncol2=17; w=11; offset=-2; strand=R; shift=5; score=47.7143; -----tawasATCAAAGgrmh ; cor=0.801; Ncor=0.518; logoDP=3.622; NIcor=0.097; NsEucl=0.905; SSD=2.175; NSW=0.901; rcor=41; rNcor=24; rlogoDP=65; rNIcor=62; rNsEucl=30; rSSD=68; rNSW=44; rank_mean=47.714; match_rank=52 a 0 0 0 0 0 17 39 25 59 3 89 5 3 97 98 96 7 20 44 35 31 c 0 0 0 0 0 23 23 22 4 35 0 0 93 0 0 0 3 18 15 25 26 g 0 0 0 0 0 24 14 17 14 57 0 0 3 0 1 2 88 53 33 16 16 t 0 0 0 0 0 35 23 36 22 4 11 95 1 3 1 2 1 9 8 24 28
1904_PB0040.1_JASPAR_CORE_2009__rc_shift5 (1904_PB0040.1_JASPAR_CORE_2009__rc)		0.805	0.521	3.773	0.092	0.905	2.177	0.901	37	22	62	65	32	70	46	47.714	53	; dyads_m3 versus 1904_PB0040.1_JASPAR_CORE_2009__rc; m=20/33; ncol2=17; w=11; offset=-2; strand=R; shift=5; score=47.7143; -----kwwasATCAAAGgrwy ; cor=0.805; Ncor=0.521; logoDP=3.773; NIcor=0.092; NsEucl=0.905; SSD=2.177; NSW=0.901; rcor=37; rNcor=22; rlogoDP=62; rNIcor=65; rNsEucl=32; rSSD=70; rNSW=46; rank_mean=47.714; match_rank=53 a 0 0 0 0 0 19 40 27 62 2 92 3 2 97 99 97 5 17 38 32 22 c 0 0 0 0 0 22 17 22 6 28 0 0 95 0 0 0 4 14 14 24 30 g 0 0 0 0 0 34 15 17 12 68 0 0 3 0 1 2 91 62 40 15 15 t 0 0 0 0 0 25 28 35 20 3 8 97 1 2 1 2 1 7 7 29 33
6753_6gat_A_3D-footprint_20130124__shift8 (6753_6gat_A_3D-footprint_20130124_)		0.805	0.439	4.748	0.415	0.862	1.377	0.885	34	52	57	48	74	27	56	49.714	57	; dyads_m3 versus 6753_6gat_A_3D-footprint_20130124_; m=21/33; ncol2=6; w=6; offset=1; strand=D; shift=8; score=49.7143; --------CnATCA------- ; cor=0.805; Ncor=0.439; logoDP=4.748; NIcor=0.415; NsEucl=0.862; SSD=1.377; NSW=0.885; rcor=34; rNcor=52; rlogoDP=57; rNIcor=48; rNsEucl=74; rSSD=27; rNSW=56; rank_mean=49.714; match_rank=57 a 0 0 0 0 0 0 0 0 11 24 67 9 0 96 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 67 24 9 11 96 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 9 24 11 9 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 9 24 9 67 0 0 0 0 0 0 0 0 0
7299_ARI3A_do_HOCOMOCO_v9__shift0 (7299_ARI3A_do_HOCOMOCO_v9_)		0.781	0.409	4.796	0.423	0.902	2.309	0.895	50	82	55	41	36	77	50	55.857	65	; dyads_m3 versus 7299_ARI3A_do_HOCOMOCO_v9_; m=22/33; ncol2=21; w=11; offset=-7; strand=D; shift=0; score=55.8571; ATTAAwyrrwATcWAAwtwww ; cor=0.781; Ncor=0.409; logoDP=4.796; NIcor=0.423; NsEucl=0.902; SSD=2.309; NSW=0.895; rcor=50; rNcor=82; rlogoDP=55; rNIcor=41; rNsEucl=36; rSSD=77; rNSW=50; rank_mean=55.857; match_rank=65 a 30 5 7 42 41 21 0 13 22 20 32 6 7 32 33 42 18 5 23 27 29 c 4 0 0 2 3 0 18 8 2 2 0 2 25 0 2 0 0 6 6 3 1 g 0 0 0 0 0 1 10 19 16 7 4 4 2 0 0 0 2 4 1 0 3 t 10 39 37 0 0 22 16 4 4 15 8 32 10 12 9 2 24 29 14 14 11
7604_RARG_f1_HOCOMOCO_v9__shift8 (7604_RARG_f1_HOCOMOCO_v9_)		0.759	0.414	7.379	0.439	0.841	1.822	0.848	75	74	30	29	81	40	79	58.286	69	; dyads_m3 versus 7604_RARG_f1_HOCOMOCO_v9_; m=23/33; ncol2=6; w=6; offset=1; strand=D; shift=8; score=58.2857; --------AGKTCA------- ; cor=0.759; Ncor=0.414; logoDP=7.379; NIcor=0.439; NsEucl=0.841; SSD=1.822; NSW=0.848; rcor=75; rNcor=74; rlogoDP=30; rNIcor=29; rNsEucl=81; rSSD=40; rNSW=79; rank_mean=58.286; match_rank=69 a 0 0 0 0 0 0 0 0 23 0 0 0 0 27 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 29 2 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 6 29 21 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 8 29 0 0 0 0 0 0 0 0 0
2619_MA0389.1_JASPAR_CORE_2009__rc_shift6 (2619_MA0389.1_JASPAR_CORE_2009__rc)		0.776	0.452	1.017	0.016	0.871	1.621	0.884	57	49	73	69	69	38	58	59.000	70	; dyads_m3 versus 2619_MA0389.1_JASPAR_CORE_2009__rc; m=24/33; ncol2=8; w=7; offset=-1; strand=R; shift=6; score= 59; ------gkAGATCt------- ; cor=0.776; Ncor=0.452; logoDP=1.017; NIcor=0.016; NsEucl=0.871; SSD=1.621; NSW=0.884; rcor=57; rNcor=49; rlogoDP=73; rNIcor=69; rNsEucl=69; rSSD=38; rNSW=58; rank_mean=59.000; match_rank=70 a 0 0 0 0 0 0 16 11 74 0 85 3 2 6 0 0 0 0 0 0 0 c 0 0 0 0 0 0 18 13 3 0 2 0 90 19 0 0 0 0 0 0 0 g 0 0 0 0 0 0 42 30 19 99 0 0 2 9 0 0 0 0 0 0 0 t 0 0 0 0 0 0 24 46 4 0 13 97 6 66 0 0 0 0 0 0 0
3893_UP00198_UniPROBE_20120919__shift2 (3893_UP00198_UniPROBE_20120919_)		0.758	0.426	6.826	0.431	0.881	2.313	0.871	79	60	35	33	59	78	69	59.000	71	; dyads_m3 versus 3893_UP00198_UniPROBE_20120919_; m=25/33; ncol2=14; w=9; offset=-5; strand=D; shift=2; score= 59; --rTGATssmATCAaw----- ; cor=0.758; Ncor=0.426; logoDP=6.826; NIcor=0.431; NsEucl=0.881; SSD=2.313; NSW=0.871; rcor=79; rNcor=60; rlogoDP=35; rNIcor=33; rNsEucl=59; rSSD=78; rNSW=69; rank_mean=59.000; match_rank=71 a 0 0 34 0.03 4 98 0.04 10 22 54 95 0.01 0 95 61 36 0 0 0 0 0 c 0 0 18 0 2 1 0 37 28 34 3 0.01 0.97 1 14 21 0 0 0 0 0 g 0 0 26 0 93 1 0.06 29 35 8 1 0 0 1 15 10 0 0 0 0 0 t 0 0 22 0.96 1 0 0.90 24 15 4 1 0.99 0.02 3 10 33 0 0 0 0 0
2872_PH0014.1_JASPAR_CORE_2009__shift2 (2872_PH0014.1_JASPAR_CORE_2009_)		0.758	0.426	6.826	0.431	0.881	2.313	0.871	79	60	35	33	59	78	69	59.000	72	; dyads_m3 versus 2872_PH0014.1_JASPAR_CORE_2009_; m=26/33; ncol2=14; w=9; offset=-5; strand=D; shift=2; score= 59; --rTGATssmATCAaw----- ; cor=0.758; Ncor=0.426; logoDP=6.826; NIcor=0.431; NsEucl=0.881; SSD=2.313; NSW=0.871; rcor=79; rNcor=60; rlogoDP=35; rNIcor=33; rNsEucl=59; rSSD=78; rNSW=69; rank_mean=59.000; match_rank=72 a 0 0 34 3 4 98 4 10 22 54 95 1 0 95 61 36 0 0 0 0 0 c 0 0 18 0 2 1 0 37 28 34 3 1 97 1 14 21 0 0 0 0 0 g 0 0 26 0 93 1 6 29 35 8 1 0 0 1 15 10 0 0 0 0 0 t 0 0 22 96 1 1 90 24 15 4 1 99 2 3 10 33 0 0 0 0 0
2760_PF0073.1_JASPAR_CORE_2009__rc_shift11 (2760_PF0073.1_JASPAR_CORE_2009__rc)		0.828	0.452	0.121	-0.177	0.857	1.471	0.877	29	50	87	87	75	33	62	60.429	74	; dyads_m3 versus 2760_PF0073.1_JASPAR_CORE_2009__rc; m=27/33; ncol2=6; w=6; offset=4; strand=R; shift=11; score=60.4286; -----------TCAAAG---- ; cor=0.828; Ncor=0.452; logoDP=0.121; NIcor=-0.177; NsEucl=0.857; SSD=1.471; NSW=0.877; rcor=29; rNcor=50; rlogoDP=87; rNIcor=87; rNsEucl=75; rSSD=33; rNSW=62; rank_mean=60.429; match_rank=74 a 0 0 0 0 0 0 0 0 0 0 0 0 0 4260 4260 4260 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 4260 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4260 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 4260 0 0 0 0 0 0 0 0 0
7300_ARI3A_f1_HOCOMOCO_v9__shift10 (7300_ARI3A_f1_HOCOMOCO_v9_)		0.764	0.417	8.757	0.415	0.831	2.058	0.829	67	70	14	47	88	53	88	61.000	75	; dyads_m3 versus 7300_ARI3A_f1_HOCOMOCO_v9_; m=28/33; ncol2=6; w=6; offset=3; strand=D; shift=10; score= 61; ----------ATTAAA----- ; cor=0.764; Ncor=0.417; logoDP=8.757; NIcor=0.415; NsEucl=0.831; SSD=2.058; NSW=0.829; rcor=67; rNcor=70; rlogoDP=14; rNIcor=47; rNsEucl=88; rSSD=53; rNSW=88; rank_mean=61.000; match_rank=75 a 0 0 0 0 0 0 0 0 0 0 47 0 0 47 47 39 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 47 47 0 0 8 0 0 0 0 0
2255_CN0092.1_JASPAR_CORE_2009__rc_shift2 (2255_CN0092.1_JASPAR_CORE_2009__rc)		0.761	0.465	4.160	0.101	0.894	2.744	0.875	72	46	61	61	48	85	66	62.714	79	; dyads_m3 versus 2255_CN0092.1_JASPAR_CORE_2009__rc; m=29/33; ncol2=18; w=11; offset=-5; strand=R; shift=2; score=62.7143; --TCTGcCAAATCAAATTAG- ; cor=0.761; Ncor=0.465; logoDP=4.160; NIcor=0.101; NsEucl=0.894; SSD=2.744; NSW=0.875; rcor=72; rNcor=46; rlogoDP=61; rNIcor=61; rNsEucl=48; rSSD=85; rNSW=66; rank_mean=62.714; match_rank=79 a 0 0 1 5 7 0 11 6 56 53 61 9 1 58 52 60 1 3 64 7 0 c 0 0 0 53 0 3 39 57 1 4 0 0 59 5 5 1 1 9 0 1 0 g 0 0 7 2 0 62 6 1 0 4 3 6 0 0 5 1 0 4 0 55 0 t 0 0 57 5 58 0 9 1 8 4 1 50 5 2 3 3 63 49 1 2 0
2559_MA0301.1_JASPAR_CORE_2009__rc_shift5 (2559_MA0301.1_JASPAR_CORE_2009__rc)		0.773	0.416	0.195	-0.115	0.872	1.606	0.885	59	73	81	78	67	36	55	64.143	81	; dyads_m3 versus 2559_MA0301.1_JASPAR_CORE_2009__rc; m=30/33; ncol2=9; w=7; offset=-2; strand=R; shift=5; score=64.1429; -----kktrGATCt------- ; cor=0.773; Ncor=0.416; logoDP=0.195; NIcor=-0.115; NsEucl=0.872; SSD=1.606; NSW=0.885; rcor=59; rNcor=73; rlogoDP=81; rNIcor=78; rNsEucl=67; rSSD=36; rNSW=55; rank_mean=64.143; match_rank=81 a 0 0 0 0 0 21 17 12 63 2 87 8 1 6 0 0 0 0 0 0 0 c 0 0 0 0 0 21 21 18 4 1 1 0 88 20 0 0 0 0 0 0 0 g 0 0 0 0 0 25 33 19 27 94 0 0 2 9 0 0 0 0 0 0 0 t 0 0 0 0 0 32 28 51 6 3 12 92 8 65 0 0 0 0 0 0 0
1838_MA0326.1_JASPAR_CORE_2009__rc_shift8 (1838_MA0326.1_JASPAR_CORE_2009__rc)		0.764	0.555	2.550	-0.043	0.862	2.447	0.847	70	17	66	72	73	81	80	65.571	82	; dyads_m3 versus 1838_MA0326.1_JASPAR_CORE_2009__rc; m=31/33; ncol2=8; w=8; offset=1; strand=R; shift=8; score=65.5714; --------yGAGCAAA----- ; cor=0.764; Ncor=0.555; logoDP=2.550; NIcor=-0.043; NsEucl=0.862; SSD=2.447; NSW=0.847; rcor=70; rNcor=17; rlogoDP=66; rNIcor=72; rNsEucl=73; rSSD=81; rNSW=80; rank_mean=65.571; match_rank=82 a 0 0 0 0 0 0 0 0 113 0 1714 0 0 1714 1451 1632 0 0 0 0 0 c 0 0 0 0 0 0 0 0 655 0 0 0 1599 0 219 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 1714 0 1714 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 958 0 0 0 115 0 89 108 0 0 0 0 0
2350_CN0187.1_JASPAR_CORE_2009__rc_shift2 (2350_CN0187.1_JASPAR_CORE_2009__rc)		0.755	0.472	4.329	0.067	0.879	2.929	0.854	81	43	59	67	61	87	76	67.714	83	; dyads_m3 versus 2350_CN0187.1_JASPAR_CORE_2009__rc; m=32/33; ncol2=15; w=10; offset=-5; strand=R; shift=2; score=67.7143; --AATGAAAGAwCAAAG---- ; cor=0.755; Ncor=0.472; logoDP=4.329; NIcor=0.067; NsEucl=0.879; SSD=2.929; NSW=0.854; rcor=81; rNcor=43; rlogoDP=59; rNIcor=67; rNsEucl=61; rSSD=87; rNSW=76; rank_mean=67.714; match_rank=83 a 0 0 47 48 0 4 40 47 47 0 44 18 0 48 46 47 0 0 0 0 0 c 0 0 0 0 0 3 2 0 0 1 0 0 41 0 2 0 1 0 0 0 0 g 0 0 1 0 0 41 5 1 0 46 1 1 2 0 0 1 47 0 0 0 0 t 0 0 0 0 48 0 1 0 1 1 3 29 5 0 0 0 0 0 0 0 0
1793_MA0235.1_JASPAR_CORE_2009__rc_shift8 (1793_MA0235.1_JASPAR_CORE_2009__rc)		0.764	0.486	0.204	-0.181	0.853	2.106	0.850	66	38	80	88	78	56	77	69.000	84	; dyads_m3 versus 1793_MA0235.1_JASPAR_CORE_2009__rc; m=33/33; ncol2=7; w=7; offset=1; strand=R; shift=8; score= 69; --------hAATCAA------ ; cor=0.764; Ncor=0.486; logoDP=0.204; NIcor=-0.181; NsEucl=0.853; SSD=2.106; NSW=0.850; rcor=66; rNcor=38; rlogoDP=80; rNIcor=88; rNsEucl=78; rSSD=56; rNSW=77; rank_mean=69.000; match_rank=84 a 0 0 0 0 0 0 0 0 6 15 15 0 0 15 12 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 4 0 0 0 15 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 5 0 0 15 0 0 1 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_shift0 ; 8 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv2_shift0 (oligos_7nt_mkv2)																		; oligos_7nt_mkv2; m=0 (reference); ncol1=11; shift=0; ncol=11; TsAGGAGTAhw ; Alignment reference a 1 1 7 0 0 7 0 0 7 2 3 c 0 2 0 0 0 0 0 0 0 2 0 g 0 3 0 7 7 0 7 0 0 0 1 t 6 1 0 0 0 0 0 7 0 3 3
5131_YufM_DBTBS_1.0__shift2 (5131_YufM_DBTBS_1.0_)		0.786	0.572	7.999	0.589	0.874	2.045	0.872	49	13	21	8	66	51	68	39.429	35	; oligos_7nt_mkv2 versus 5131_YufM_DBTBS_1.0_; m=1/7; ncol2=8; w=8; offset=2; strand=D; shift=2; score=39.4286; --ArGrGdws- ; cor=0.786; Ncor=0.572; logoDP=7.999; NIcor=0.589; NsEucl=0.874; SSD=2.045; NSW=0.872; rcor=49; rNcor=13; rlogoDP=21; rNIcor=8; rNsEucl=66; rSSD=51; rNSW=68; rank_mean=39.429; match_rank=35 a 0 0 3 1 0 2 0 1 2 0 0 c 0 0 0 0 0 0 0 0 0 1 0 g 0 0 0 2 3 1 3 1 0 2 0 t 0 0 0 0 0 0 0 1 1 0 0
5047_ZmHOX2a_1__Athamap_20091028__rc_shift0 (5047_ZmHOX2a_1__Athamap_20091028__rc)		0.825	0.525	0.129	-0.139	0.881	1.382	0.901	31	19	84	81	57	28	43	49.000	55	; oligos_7nt_mkv2 versus 5047_ZmHOX2a_1__Athamap_20091028__rc; m=2/7; ncol2=7; w=7; offset=0; strand=R; shift=0; score= 49; ttAGGAy---- ; cor=0.825; Ncor=0.525; logoDP=0.129; NIcor=-0.139; NsEucl=0.881; SSD=1.382; NSW=0.901; rcor=31; rNcor=19; rlogoDP=84; rNIcor=81; rNsEucl=57; rSSD=28; rNSW=43; rank_mean=49.000; match_rank=55 a 8 6 38 0 0 38 7 0 0 0 0 c 3 8 0 0 0 0 16 0 0 0 0 g 6 7 0 38 38 0 4 0 0 0 0 t 21 17 0 0 0 0 11 0 0 0 0
2780_PF0093.1_JASPAR_CORE_2009__shift3 (2780_PF0093.1_JASPAR_CORE_2009_)		0.778	0.424	9.609	0.424	0.833	2.000	0.833	54	62	10	39	85	46	85	54.429	63	; oligos_7nt_mkv2 versus 2780_PF0093.1_JASPAR_CORE_2009_; m=3/7; ncol2=6; w=6; offset=3; strand=D; shift=3; score=54.4286; ---GGATTA-- ; cor=0.778; Ncor=0.424; logoDP=9.609; NIcor=0.424; NsEucl=0.833; SSD=2.000; NSW=0.833; rcor=54; rNcor=62; rlogoDP=10; rNIcor=39; rNsEucl=85; rSSD=46; rNSW=85; rank_mean=54.429; match_rank=63 a 0 0 0 0 0 1992 0 0 1992 0 0 c 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 1992 1992 0 0 0 0 0 0 t 0 0 0 0 0 0 1992 1992 0 0 0
3094_NarL_RegulonDB_7.5__shift1 (3094_NarL_RegulonDB_7.5_)		0.764	0.555	4.299	0.537	0.866	2.289	0.857	71	18	60	15	71	76	73	54.857	64	; oligos_7nt_mkv2 versus 3094_NarL_RegulonDB_7.5_; m=4/7; ncol2=8; w=8; offset=1; strand=D; shift=1; score=54.8571; -wakrrkTA-- ; cor=0.764; Ncor=0.555; logoDP=4.299; NIcor=0.537; NsEucl=0.866; SSD=2.289; NSW=0.857; rcor=71; rNcor=18; rlogoDP=60; rNIcor=15; rNsEucl=71; rSSD=76; rNSW=73; rank_mean=54.857; match_rank=64 a 0 38 54 8 25 41 9 0 86 0 0 c 0 4 9 0 12 5 0 4 0 0 0 g 0 17 15 36 45 45 54 2 0 0 0 t 0 32 13 47 9 0 28 85 5 0 0
3095_NarP_RegulonDB_7.5__rc_shift2 (3095_NarP_RegulonDB_7.5__rc)		0.789	0.574	0.939	-0.161	0.874	2.044	0.872	48	12	74	83	65	50	67	57.000	68	; oligos_7nt_mkv2 versus 3095_NarP_RegulonDB_7.5__rc; m=5/7; ncol2=8; w=8; offset=2; strand=R; shift=2; score= 57; --AgrrGTAk- ; cor=0.789; Ncor=0.574; logoDP=0.939; NIcor=-0.161; NsEucl=0.874; SSD=2.044; NSW=0.872; rcor=48; rNcor=12; rlogoDP=74; rNIcor=83; rNsEucl=65; rSSD=50; rNSW=67; rank_mean=57.000; match_rank=68 a 0 0 14 4 5 6 0 0 20 2 0 c 0 0 3 0 2 1 0 2 0 0 0 g 0 0 2 12 10 13 16 0 0 9 0 t 0 0 1 4 3 0 4 18 0 9 0
1771_MA0212.1_JASPAR_CORE_2009__rc_shift3 (1771_MA0212.1_JASPAR_CORE_2009__rc)		0.767	0.418	1.998	-0.055	0.832	2.025	0.831	63	68	70	74	86	48	86	70.714	85	; oligos_7nt_mkv2 versus 1771_MA0212.1_JASPAR_CORE_2009__rc; m=6/7; ncol2=6; w=6; offset=3; strand=R; shift=3; score=70.7143; ---GGATTA-- ; cor=0.767; Ncor=0.418; logoDP=1.998; NIcor=-0.055; NsEucl=0.832; SSD=2.025; NSW=0.831; rcor=63; rNcor=68; rlogoDP=70; rNIcor=74; rNsEucl=86; rSSD=48; rNSW=86; rank_mean=70.714; match_rank=85 a 0 0 0 1 0 21 0 2 22 0 0 c 0 0 0 0 0 1 0 0 0 0 0 g 0 0 0 21 22 0 0 0 0 0 0 t 0 0 0 0 0 0 22 20 0 0 0
1792_MA0234.1_JASPAR_CORE_2009__rc_shift3 (1792_MA0234.1_JASPAR_CORE_2009__rc)		0.764	0.417	2.075	-0.055	0.832	2.039	0.830	68	71	69	73	87	49	87	72.000	87	; oligos_7nt_mkv2 versus 1792_MA0234.1_JASPAR_CORE_2009__rc; m=7/7; ncol2=6; w=6; offset=3; strand=R; shift=3; score= 72; ---GGATTA-- ; cor=0.764; Ncor=0.417; logoDP=2.075; NIcor=-0.055; NsEucl=0.832; SSD=2.039; NSW=0.830; rcor=68; rNcor=71; rlogoDP=69; rNIcor=73; rNsEucl=87; rSSD=49; rNSW=87; rank_mean=72.000; match_rank=87 a 0 0 0 1 0 17 0 0 19 0 0 c 0 0 0 1 0 2 0 0 0 0 0 g 0 0 0 17 19 0 0 0 0 0 0 t 0 0 0 0 0 0 19 19 0 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_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_8nt_mkv2_shift0 (oligos_8nt_mkv2)																		; oligos_8nt_mkv2; m=0 (reference); ncol1=12; shift=0; ncol=13; rwAGAGGGAGws- ; Alignment reference a 2 2 3 0 3 0 0 0 3 0 1 0 0 c 0 0 0 0 0 0 0 0 0 0 0 2 0 g 1 0 0 3 0 3 3 3 0 3 0 1 0 t 0 1 0 0 0 0 0 0 0 0 2 0 0
6513_2v2t_A_3D-footprint_20130124__shift5 (6513_2v2t_A_3D-footprint_20130124_)		0.860	0.430	4.825	0.409	0.876	1.103	0.908	22	57	53	50	63	17	35	42.429	39	; oligos_8nt_mkv2 versus 6513_2v2t_A_3D-footprint_20130124_; m=1/3; ncol2=6; w=6; offset=5; strand=D; shift=5; score=42.4286; -----GGgAnT-- ; cor=0.860; Ncor=0.430; logoDP=4.825; NIcor=0.409; NsEucl=0.876; SSD=1.103; NSW=0.908; rcor=22; rNcor=57; rlogoDP=53; rNIcor=50; rNsEucl=63; rSSD=17; rNSW=35; rank_mean=42.429; match_rank=39 a 0 0 0 0 0 0 0 17 69 24 11 0 0 c 0 0 0 0 0 0 0 10 11 24 8 0 0 g 0 0 0 0 0 96 96 61 8 24 8 0 0 t 0 0 0 0 0 0 0 8 8 24 69 0 0
6322_1svc_P_3D-footprint_20130124__rc_shift5 (6322_1svc_P_3D-footprint_20130124__rc)		0.829	0.483	0.244	-0.041	0.881	1.387	0.901	28	40	79	71	58	29	47	50.286	58	; oligos_8nt_mkv2 versus 6322_1svc_P_3D-footprint_20130124__rc; m=2/3; ncol2=7; w=7; offset=5; strand=R; shift=5; score=50.2857; -----gGGAnnc- ; cor=0.829; Ncor=0.483; logoDP=0.244; NIcor=-0.041; NsEucl=0.881; SSD=1.387; NSW=0.901; rcor=28; rNcor=40; rlogoDP=79; rNIcor=71; rNsEucl=58; rSSD=29; rNSW=47; rank_mean=50.286; match_rank=58 a 0 0 0 0 0 13 0 0 96 24 24 13 0 c 0 0 0 0 0 13 0 0 0 24 24 54 0 g 0 0 0 0 0 54 96 96 0 24 24 16 0 t 0 0 0 0 0 16 0 0 0 24 24 13 0
2711_PF0024.1_JASPAR_CORE_2009__shift5 (2711_PF0024.1_JASPAR_CORE_2009_)		0.758	0.408	9.734	0.441	0.849	2.222	0.841	77	83	8	28	80	71	82	61.286	76	; oligos_8nt_mkv2 versus 2711_PF0024.1_JASPAR_CORE_2009_; m=3/3; ncol2=8; w=7; offset=5; strand=D; shift=5; score=61.2857; -----GGGAGGrG ; cor=0.758; Ncor=0.408; logoDP=9.734; NIcor=0.441; NsEucl=0.849; SSD=2.222; NSW=0.841; rcor=77; rNcor=83; rlogoDP=8; rNIcor=28; rNsEucl=80; rSSD=71; rNSW=82; rank_mean=61.286; match_rank=76 a 0 0 0 0 0 0 0 0 11176 0 0 3724 2525 c 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 11176 11176 11176 0 11176 11176 7452 8651 t 0 0 0 0 0 0 0 0 0 0 0 0 0