One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163848_zCfwD2/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -format2 tf -strand DR -lth cor 0.7 -lth Ncor 0.4 -uth match_rank 50 -return cor,Ncor,logoDP,NsEucl,NSW,match_rank,matrix_id,matrix_name,width,strand,offset,consensus,alignments_1ton -o $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163848_zCfwD2/compare-matrices.tab

One-to-n matrix alignment; reference matrix: cluster_5_shift0 ; 7 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NsEucl NSW rcor rNcor rlogoDP rNsEucl rNSW rank_mean match_rank Aligned matrices
cluster_5_shift0 (cluster_5)
; cluster_5; m=0 (reference); ncol1=12; shift=0; ncol=12; wwATACGTATww ; Alignment reference a 682 442 1350 64 1375 82 247 46 1353 53 560 404 c 179 267 32 42 30 1117 30 25 17 41 207 211 g 211 207 41 17 25 30 1117 30 42 32 267 179 t 404 560 53 1353 46 247 82 1375 64 1350 442 682

bZIP65_EEAD0071_EEADannot_shift3 (bZIP65:EEAD0071:EEADannot) 0.988 0.494 6.670 0.946 0.982 1 4 1 1 1 1.600 1
; cluster_5 versus bZIP65_EEAD0071_EEADannot (bZIP65:EEAD0071:EEADannot); m=1/6; ncol2=6; w=0; offset=3; strand=D; shift=3; score= 1.6; ---TACGTA--- ; cor=0.988; Ncor=0.494; logoDP=6.670; NsEucl=0.946; NSW=0.982; rcor=1; rNcor=4; rlogoDP=1; rNsEucl=1; rNSW=1; rank_mean=1.600; match_rank=1 a 0 0 0 0 1 0 0 0 1 0 0 0 c 0 0 0 0 0 1 0 0 0 0 0 0 g 0 0 0 0 0 0 1 0 0 0 0 0 t 0 0 0 1 0 0 0 1 0 0 0 0

ANAC55_ANAC55_2_ArabidopsisPBM_shift1 (ANAC55:ANAC55_2:ArabidopsisPBM) 0.740 0.617 3.436 0.898 0.896 4 1 4 2 4 3.000 2
; cluster_5 versus ANAC55_ANAC55_2_ArabidopsisPBM (ANAC55:ANAC55_2:ArabidopsisPBM); m=2/6; ncol2=10; w=0; offset=1; strand=D; shift=1; score= 3; -rwTACGTAwy- ; cor=0.740; Ncor=0.617; logoDP=3.436; NsEucl=0.898; NSW=0.896; rcor=4; rNcor=1; rlogoDP=4; rNsEucl=2; rNSW=4; rank_mean=3.000; match_rank=2 a 0 39 27 3 89 5 5 2 70 64 6 0 c 0 11 3 22 5 88 2 4 4 6 32 0 g 0 30 6 4 4 2 88 5 23 3 7 0 t 0 20 64 71 2 5 5 89 3 27 55 0

ARR18_MA0948.2_JASPAR_shift0 (ARR18:MA0948.2:JASPAR) 0.818 0.477 3.426 0.892 0.918 2 5 5 3 2 3.400 3
; cluster_5 versus ARR18_MA0948.2_JASPAR (ARR18:MA0948.2:JASPAR); m=3/6; ncol2=7; w=0; offset=0; strand=D; shift=0; score= 3.4; AGATAcG----- ; cor=0.818; Ncor=0.477; logoDP=3.426; NsEucl=0.892; NSW=0.918; rcor=2; rNcor=5; rlogoDP=5; rNsEucl=3; rNSW=2; rank_mean=3.400; match_rank=3 a 834 0 999 0 728 48 159 0 0 0 0 0 c 25 88 0 0 25 673 72 0 0 0 0 0 g 25 912 0 0 25 48 697 0 0 0 0 0 t 115 0 0 999 222 231 72 0 0 0 0 0

ZFHD10-3_EEAD0065_EEADannot_shift1 (ZFHD10-3:EEAD0065:EEADannot) 0.710 0.592 5.719 0.878 0.851 5 2 2 6 6 4.200 4
; cluster_5 versus ZFHD10-3_EEAD0065_EEADannot (ZFHD10-3:EEAD0065:EEADannot); m=4/6; ncol2=10; w=0; offset=1; strand=D; shift=1; score= 4.2; -TATATATATA- ; cor=0.710; Ncor=0.592; logoDP=5.719; NsEucl=0.878; NSW=0.851; rcor=5; rNcor=2; rlogoDP=2; rNsEucl=6; rNSW=6; rank_mean=4.200; match_rank=4 a 0 10 90 10 90 10 90 10 90 10 90 0 c 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 t 0 90 10 90 10 90 10 90 10 90 10 0

AtHB32.DAP_M0856_AthalianaCistrome_shift2 (AtHB32.DAP:M0856:AthalianaCistrome) 0.700 0.539 3.456 0.890 0.880 6 3 3 4 5 4.200 5
; cluster_5 versus AtHB32.DAP_M0856_AthalianaCistrome (AtHB32.DAP:M0856:AthalianaCistrome); m=5/6; ncol2=11; w=0; offset=2; strand=D; shift=2; score= 4.2; --wwwCGhATwW ; cor=0.700; Ncor=0.539; logoDP=3.456; NsEucl=0.890; NSW=0.880; rcor=6; rNcor=3; rlogoDP=3; rNsEucl=4; rNSW=5; rank_mean=4.200; match_rank=5 a 0 0 368 361 211 14 59 194 509 0 250 429 c 0 0 34 19 82 519 0 237 0 0 15 4 g 0 0 22 20 47 20 533 2 91 0 24 0 t 0 0 176 200 260 47 8 167 0 600 311 167

ARR11_MA0946.1_JASPAR_rc_shift5 (ARR11:MA0946.1:JASPAR_rc) 0.815 0.439 2.644 0.879 0.897 3 6 6 5 3 4.600 6
; cluster_5 versus ARR11_MA0946.1_JASPAR_rc (ARR11:MA0946.1:JASPAR_rc); m=6/6; ncol2=8; w=0; offset=5; strand=R; shift=5; score= 4.6; -----CGTATCT ; cor=0.815; Ncor=0.439; logoDP=2.644; NsEucl=0.879; NSW=0.897; rcor=3; rNcor=6; rlogoDP=6; rNsEucl=5; rNSW=3; rank_mean=4.600; match_rank=6 a 0 0 0 0 0 13 162 242 987 4 11 32 c 0 0 0 0 0 968 2 4 2 4 982 29 g 0 0 0 0 0 5 833 22 3 2 2 11 t 0 0 0 0 0 14 3 732 7 989 5 927

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
cluster_5_shift0 (cluster_5)													; cluster_5; m=0 (reference); ncol1=12; shift=0; ncol=12; wwATACGTATww ; Alignment reference a 682 442 1350 64 1375 82 247 46 1353 53 560 404 c 179 267 32 42 30 1117 30 25 17 41 207 211 g 211 207 41 17 25 30 1117 30 42 32 267 179 t 404 560 53 1353 46 247 82 1375 64 1350 442 682
bZIP65_EEAD0071_EEADannot_shift3 (bZIP65:EEAD0071:EEADannot)	0.988	0.494	6.670	0.946	0.982	1	4	1	1	1	1.600	1	; cluster_5 versus bZIP65_EEAD0071_EEADannot (bZIP65:EEAD0071:EEADannot); m=1/6; ncol2=6; w=0; offset=3; strand=D; shift=3; score= 1.6; ---TACGTA--- ; cor=0.988; Ncor=0.494; logoDP=6.670; NsEucl=0.946; NSW=0.982; rcor=1; rNcor=4; rlogoDP=1; rNsEucl=1; rNSW=1; rank_mean=1.600; match_rank=1 a 0 0 0 0 1 0 0 0 1 0 0 0 c 0 0 0 0 0 1 0 0 0 0 0 0 g 0 0 0 0 0 0 1 0 0 0 0 0 t 0 0 0 1 0 0 0 1 0 0 0 0
ANAC55_ANAC55_2_ArabidopsisPBM_shift1 (ANAC55:ANAC55_2:ArabidopsisPBM)	0.740	0.617	3.436	0.898	0.896	4	1	4	2	4	3.000	2	; cluster_5 versus ANAC55_ANAC55_2_ArabidopsisPBM (ANAC55:ANAC55_2:ArabidopsisPBM); m=2/6; ncol2=10; w=0; offset=1; strand=D; shift=1; score= 3; -rwTACGTAwy- ; cor=0.740; Ncor=0.617; logoDP=3.436; NsEucl=0.898; NSW=0.896; rcor=4; rNcor=1; rlogoDP=4; rNsEucl=2; rNSW=4; rank_mean=3.000; match_rank=2 a 0 39 27 3 89 5 5 2 70 64 6 0 c 0 11 3 22 5 88 2 4 4 6 32 0 g 0 30 6 4 4 2 88 5 23 3 7 0 t 0 20 64 71 2 5 5 89 3 27 55 0
ARR18_MA0948.2_JASPAR_shift0 (ARR18:MA0948.2:JASPAR)	0.818	0.477	3.426	0.892	0.918	2	5	5	3	2	3.400	3	; cluster_5 versus ARR18_MA0948.2_JASPAR (ARR18:MA0948.2:JASPAR); m=3/6; ncol2=7; w=0; offset=0; strand=D; shift=0; score= 3.4; AGATAcG----- ; cor=0.818; Ncor=0.477; logoDP=3.426; NsEucl=0.892; NSW=0.918; rcor=2; rNcor=5; rlogoDP=5; rNsEucl=3; rNSW=2; rank_mean=3.400; match_rank=3 a 834 0 999 0 728 48 159 0 0 0 0 0 c 25 88 0 0 25 673 72 0 0 0 0 0 g 25 912 0 0 25 48 697 0 0 0 0 0 t 115 0 0 999 222 231 72 0 0 0 0 0
ZFHD10-3_EEAD0065_EEADannot_shift1 (ZFHD10-3:EEAD0065:EEADannot)	0.710	0.592	5.719	0.878	0.851	5	2	2	6	6	4.200	4	; cluster_5 versus ZFHD10-3_EEAD0065_EEADannot (ZFHD10-3:EEAD0065:EEADannot); m=4/6; ncol2=10; w=0; offset=1; strand=D; shift=1; score= 4.2; -TATATATATA- ; cor=0.710; Ncor=0.592; logoDP=5.719; NsEucl=0.878; NSW=0.851; rcor=5; rNcor=2; rlogoDP=2; rNsEucl=6; rNSW=6; rank_mean=4.200; match_rank=4 a 0 10 90 10 90 10 90 10 90 10 90 0 c 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 t 0 90 10 90 10 90 10 90 10 90 10 0
AtHB32.DAP_M0856_AthalianaCistrome_shift2 (AtHB32.DAP:M0856:AthalianaCistrome)	0.700	0.539	3.456	0.890	0.880	6	3	3	4	5	4.200	5	; cluster_5 versus AtHB32.DAP_M0856_AthalianaCistrome (AtHB32.DAP:M0856:AthalianaCistrome); m=5/6; ncol2=11; w=0; offset=2; strand=D; shift=2; score= 4.2; --wwwCGhATwW ; cor=0.700; Ncor=0.539; logoDP=3.456; NsEucl=0.890; NSW=0.880; rcor=6; rNcor=3; rlogoDP=3; rNsEucl=4; rNSW=5; rank_mean=4.200; match_rank=5 a 0 0 368 361 211 14 59 194 509 0 250 429 c 0 0 34 19 82 519 0 237 0 0 15 4 g 0 0 22 20 47 20 533 2 91 0 24 0 t 0 0 176 200 260 47 8 167 0 600 311 167
ARR11_MA0946.1_JASPAR_rc_shift5 (ARR11:MA0946.1:JASPAR_rc)	0.815	0.439	2.644	0.879	0.897	3	6	6	5	3	4.600	6	; cluster_5 versus ARR11_MA0946.1_JASPAR_rc (ARR11:MA0946.1:JASPAR_rc); m=6/6; ncol2=8; w=0; offset=5; strand=R; shift=5; score= 4.6; -----CGTATCT ; cor=0.815; Ncor=0.439; logoDP=2.644; NsEucl=0.879; NSW=0.897; rcor=3; rNcor=6; rlogoDP=6; rNsEucl=5; rNSW=3; rank_mean=4.600; match_rank=6 a 0 0 0 0 0 13 162 242 987 4 11 32 c 0 0 0 0 0 968 2 4 2 4 982 29 g 0 0 0 0 0 5 833 22 3 2 2 11 t 0 0 0 0 0 14 3 732 7 989 5 927