One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/02/26/compare-matrices_2026-02-26.141129_glP3y4/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_plants_non-redundant_pfms_transfac.txt -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/2026/02/26/compare-matrices_2026-02-26.141129_glP3y4/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 6 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
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; wrCATGCAtr ; Alignment reference a 13 15 0 46 0 0 0 41 12 18 c 12 8 49 0 3 0 50 3 8 6 g 5 17 0 2 0 50 0 2 4 14 t 20 10 1 2 47 0 0 4 26 12

MA0581.2_shift2 (LEC2) 0.982 0.589 8.457 0.955 0.988 1 3 2 1 1 1.600 1
; dyads_m3 versus MA0581.2 (LEC2); m=1/5; ncol2=6; w=0; offset=2; strand=D; shift=2; score= 1.6; --CATGCr-- ; cor=0.982; Ncor=0.589; logoDP=8.457; NsEucl=0.955; NSW=0.988; rcor=1; rNcor=3; rlogoDP=2; rNsEucl=1; rNSW=1; rank_mean=1.600; match_rank=1 a 0 0 2.0 487.0 0.0 0.0 0.0 301.0 0 0 c 0 0 475.0 0.0 0.0 0.0 487.0 30.0 0 0 g 0 0 0.0 0.0 0.0 487.0 0.0 156.0 0 0 t 0 0 10.0 0.0 487.0 0.0 0.0 0.0 0 0

MA0564.2_rc_shift1 (ABI3_rc) 0.945 0.567 6.429 0.926 0.967 2 4 3 3 2 2.800 2
; dyads_m3 versus MA0564.2_rc (ABI3_rc); m=2/5; ncol2=6; w=0; offset=1; strand=R; shift=1; score= 2.8; -GCATGC--- ; cor=0.945; Ncor=0.567; logoDP=6.429; NsEucl=0.926; NSW=0.967; rcor=2; rNcor=4; rlogoDP=3; rNsEucl=3; rNSW=2; rank_mean=2.800; match_rank=2 a 0 2.0 1.0 97.0 1.0 1.0 5.0 0 0 0 c 0 8.0 96.0 1.0 1.0 2.0 85.0 0 0 0 g 0 84.0 1.0 1.0 1.0 96.0 7.0 0 0 0 t 0 6.0 1.0 1.0 97.0 1.0 3.0 0 0 0

MA0565.3_shift1 (FUS3) 0.930 0.651 8.912 0.915 0.950 3 2 1 4 4 2.800 3
; dyads_m3 versus MA0565.3 (FUS3); m=3/5; ncol2=7; w=0; offset=1; strand=D; shift=1; score= 2.8; -ACATGCA-- ; cor=0.930; Ncor=0.651; logoDP=8.912; NsEucl=0.915; NSW=0.950; rcor=3; rNcor=2; rlogoDP=1; rNsEucl=4; rNSW=4; rank_mean=2.800; match_rank=3 a 0 1146.0 0.0 1141.0 3.0 0.0 0.0 1055.0 0 0 c 0 0.0 1146.0 2.0 5.0 1.0 1146.0 18.0 0 0 g 0 0.0 0.0 2.0 1.0 1145.0 0.0 28.0 0 0 t 0 0.0 0.0 1.0 1137.0 0.0 0.0 45.0 0 0

MA1810.2_rc_shift0 (GLYMA-08G357600_rc) 0.927 0.834 0.265 0.935 0.962 4 1 5 2 3 3.000 4
; dyads_m3 versus MA1810.2_rc (GLYMA-08G357600_rc); m=4/5; ncol2=9; w=0; offset=0; strand=R; shift=0; score= 3; TGCATGCAt- ; cor=0.927; Ncor=0.834; logoDP=0.265; NsEucl=0.935; NSW=0.962; rcor=4; rNcor=1; rlogoDP=5; rNsEucl=2; rNSW=3; rank_mean=3.000; match_rank=4 a 14.0 10.0 4.0 178.0 2.0 6.0 3.0 159.0 34.0 0 c 9.0 8.0 179.0 1.0 2.0 1.0 172.0 10.0 24.0 0 g 8.0 163.0 4.0 3.0 2.0 177.0 10.0 7.0 11.0 0 t 158.0 8.0 2.0 7.0 183.0 5.0 4.0 13.0 120.0 0

MA2047.2_shift2 (NAC037) 0.711 0.497 5.533 0.846 0.833 5 5 4 5 5 4.800 5
; dyads_m3 versus MA2047.2 (NAC037); m=5/5; ncol2=7; w=0; offset=2; strand=D; shift=2; score= 4.8; --CAAGCAA- ; cor=0.711; Ncor=0.497; logoDP=5.533; NsEucl=0.846; NSW=0.833; rcor=5; rNcor=5; rlogoDP=4; rNsEucl=5; rNSW=5; rank_mean=4.800; match_rank=5 a 0 0 25.0 1919.0 1709.0 6.0 4.0 1725.0 1827.0 0 c 0 0 1779.0 22.0 217.0 24.0 1727.0 85.0 16.0 0 g 0 0 32.0 17.0 14.0 1928.0 32.0 56.0 24.0 0 t 0 0 151.0 29.0 47.0 29.0 224.0 121.0 120.0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m3_shift0 (dyads_m3)													; dyads_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; wrCATGCAtr ; Alignment reference a 13 15 0 46 0 0 0 41 12 18 c 12 8 49 0 3 0 50 3 8 6 g 5 17 0 2 0 50 0 2 4 14 t 20 10 1 2 47 0 0 4 26 12
MA0581.2_shift2 (LEC2)	0.982	0.589	8.457	0.955	0.988	1	3	2	1	1	1.600	1	; dyads_m3 versus MA0581.2 (LEC2); m=1/5; ncol2=6; w=0; offset=2; strand=D; shift=2; score= 1.6; --CATGCr-- ; cor=0.982; Ncor=0.589; logoDP=8.457; NsEucl=0.955; NSW=0.988; rcor=1; rNcor=3; rlogoDP=2; rNsEucl=1; rNSW=1; rank_mean=1.600; match_rank=1 a 0 0 2.0 487.0 0.0 0.0 0.0 301.0 0 0 c 0 0 475.0 0.0 0.0 0.0 487.0 30.0 0 0 g 0 0 0.0 0.0 0.0 487.0 0.0 156.0 0 0 t 0 0 10.0 0.0 487.0 0.0 0.0 0.0 0 0
MA0564.2_rc_shift1 (ABI3_rc)	0.945	0.567	6.429	0.926	0.967	2	4	3	3	2	2.800	2	; dyads_m3 versus MA0564.2_rc (ABI3_rc); m=2/5; ncol2=6; w=0; offset=1; strand=R; shift=1; score= 2.8; -GCATGC--- ; cor=0.945; Ncor=0.567; logoDP=6.429; NsEucl=0.926; NSW=0.967; rcor=2; rNcor=4; rlogoDP=3; rNsEucl=3; rNSW=2; rank_mean=2.800; match_rank=2 a 0 2.0 1.0 97.0 1.0 1.0 5.0 0 0 0 c 0 8.0 96.0 1.0 1.0 2.0 85.0 0 0 0 g 0 84.0 1.0 1.0 1.0 96.0 7.0 0 0 0 t 0 6.0 1.0 1.0 97.0 1.0 3.0 0 0 0
MA0565.3_shift1 (FUS3)	0.930	0.651	8.912	0.915	0.950	3	2	1	4	4	2.800	3	; dyads_m3 versus MA0565.3 (FUS3); m=3/5; ncol2=7; w=0; offset=1; strand=D; shift=1; score= 2.8; -ACATGCA-- ; cor=0.930; Ncor=0.651; logoDP=8.912; NsEucl=0.915; NSW=0.950; rcor=3; rNcor=2; rlogoDP=1; rNsEucl=4; rNSW=4; rank_mean=2.800; match_rank=3 a 0 1146.0 0.0 1141.0 3.0 0.0 0.0 1055.0 0 0 c 0 0.0 1146.0 2.0 5.0 1.0 1146.0 18.0 0 0 g 0 0.0 0.0 2.0 1.0 1145.0 0.0 28.0 0 0 t 0 0.0 0.0 1.0 1137.0 0.0 0.0 45.0 0 0
MA1810.2_rc_shift0 (GLYMA-08G357600_rc)	0.927	0.834	0.265	0.935	0.962	4	1	5	2	3	3.000	4	; dyads_m3 versus MA1810.2_rc (GLYMA-08G357600_rc); m=4/5; ncol2=9; w=0; offset=0; strand=R; shift=0; score= 3; TGCATGCAt- ; cor=0.927; Ncor=0.834; logoDP=0.265; NsEucl=0.935; NSW=0.962; rcor=4; rNcor=1; rlogoDP=5; rNsEucl=2; rNSW=3; rank_mean=3.000; match_rank=4 a 14.0 10.0 4.0 178.0 2.0 6.0 3.0 159.0 34.0 0 c 9.0 8.0 179.0 1.0 2.0 1.0 172.0 10.0 24.0 0 g 8.0 163.0 4.0 3.0 2.0 177.0 10.0 7.0 11.0 0 t 158.0 8.0 2.0 7.0 183.0 5.0 4.0 13.0 120.0 0
MA2047.2_shift2 (NAC037)	0.711	0.497	5.533	0.846	0.833	5	5	4	5	5	4.800	5	; dyads_m3 versus MA2047.2 (NAC037); m=5/5; ncol2=7; w=0; offset=2; strand=D; shift=2; score= 4.8; --CAAGCAA- ; cor=0.711; Ncor=0.497; logoDP=5.533; NsEucl=0.846; NSW=0.833; rcor=5; rNcor=5; rlogoDP=4; rNsEucl=5; rNSW=5; rank_mean=4.800; match_rank=5 a 0 0 25.0 1919.0 1709.0 6.0 4.0 1725.0 1827.0 0 c 0 0 1779.0 22.0 217.0 24.0 1727.0 85.0 16.0 0 g 0 0 32.0 17.0 14.0 1928.0 32.0 56.0 24.0 0 t 0 0 151.0 29.0 47.0 29.0 224.0 121.0 120.0 0