One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.114837_c3UFLS/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/2026/04/09/compare-matrices_2026-04-09.114837_c3UFLS/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift0 ; 5 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
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; wtCGATTTCGww ; Alignment reference a 660 547 124 157 2400 128 61 63 68 221 880 673 c 445 537 2225 46 38 52 103 108 2190 102 467 613 g 480 393 72 2333 65 33 75 40 137 2052 480 453 t 1004 1112 168 53 86 2376 2350 2378 194 214 762 850

AT3G49930.DAP_M0336_AthalianaCistrome_rc_shift2 (AT3G49930.DAP:M0336:AthalianaCistrome_rc) 0.899 0.525 2.584 0.906 0.939 1 2 3 2 1 1.800 1
; oligos_7nt_mkv5_m1 versus AT3G49930.DAP_M0336_AthalianaCistrome_rc (AT3G49930.DAP:M0336:AthalianaCistrome_rc); m=1/4; ncol2=7; w=0; offset=2; strand=R; shift=2; score= 1.8; --wGATTTC--- ; cor=0.899; Ncor=0.525; logoDP=2.584; NsEucl=0.906; NSW=0.939; rcor=1; rNcor=2; rlogoDP=3; rNsEucl=2; rNSW=1; rank_mean=1.800; match_rank=1 a 0 0 46 0 96 0 0 0 0 0 0 0 c 0 0 12 0 6 0 0 0 102 0 0 0 g 0 0 14 102 0 0 0 0 0 0 0 0 t 0 0 30 0 0 102 102 102 0 0 0 0

AT5G22990.DAP_M0312_AthalianaCistrome_shift1 (AT5G22990.DAP:M0312:AthalianaCistrome) 0.760 0.522 4.145 0.909 0.909 3 3 1 1 2 2.000 2
; oligos_7nt_mkv5_m1 versus AT5G22990.DAP_M0312_AthalianaCistrome (AT5G22990.DAP:M0312:AthalianaCistrome); m=2/4; ncol2=15; w=0; offset=1; strand=D; shift=1; score= 2; -wCGwcwTCGwy ; cor=0.760; Ncor=0.522; logoDP=4.145; NsEucl=0.909; NSW=0.909; rcor=3; rNcor=3; rlogoDP=1; rNsEucl=1; rNSW=2; rank_mean=2.000; match_rank=2 a 0 169 0 32 220 133 249 44 0 17 232 81 c 0 79 571 2 13 269 3 51 584 4 25 187 g 0 10 0 528 28 41 108 2 0 547 20 41 t 0 326 13 22 323 141 224 487 0 16 307 275

APRR2_M1332_1.02_CISBP_rc_shift1 (APRR2:M1332_1.02:CISBP_rc) 0.767 0.639 1.269 0.903 0.906 2 1 4 3 3 2.600 3
; oligos_7nt_mkv5_m1 versus APRR2_M1332_1.02_CISBP_rc (APRR2:M1332_1.02:CISBP_rc); m=3/4; ncol2=10; w=0; offset=1; strand=R; shift=1; score= 2.6; -trGATtwysy- ; cor=0.767; Ncor=0.639; logoDP=1.269; NsEucl=0.903; NSW=0.906; rcor=2; rNcor=1; rlogoDP=4; rNsEucl=3; rNSW=3; rank_mean=2.600; match_rank=3 a 0 20 44 8 85 10 20 28 8 21 22 0 c 0 24 13 7 0 1 12 20 53 25 30 0 g 0 22 28 71 4 2 5 22 12 38 18 0 t 0 34 15 14 11 87 63 30 27 16 30 0

TIFY2A_M0760_1.02_CISBP_shift1 (TIFY2A:M0760_1.02:CISBP) 0.705 0.411 2.886 0.866 0.874 4 4 2 4 4 3.600 4
; oligos_7nt_mkv5_m1 versus TIFY2A_M0760_1.02_CISBP (TIFY2A:M0760_1.02:CISBP); m=4/4; ncol2=7; w=0; offset=1; strand=D; shift=1; score= 3.6; -haGATsd---- ; cor=0.705; Ncor=0.411; logoDP=2.886; NsEucl=0.866; NSW=0.874; rcor=4; rNcor=4; rlogoDP=2; rNsEucl=4; rNSW=4; rank_mean=3.600; match_rank=4 a 0 26 40 8 92 1 13 26 0 0 0 0 c 0 25 24 1 0 0 32 20 0 0 0 0 g 0 23 13 86 1 0 31 26 0 0 0 0 t 0 26 23 5 7 99 24 28 0 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1)													; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; wtCGATTTCGww ; Alignment reference a 660 547 124 157 2400 128 61 63 68 221 880 673 c 445 537 2225 46 38 52 103 108 2190 102 467 613 g 480 393 72 2333 65 33 75 40 137 2052 480 453 t 1004 1112 168 53 86 2376 2350 2378 194 214 762 850
AT3G49930.DAP_M0336_AthalianaCistrome_rc_shift2 (AT3G49930.DAP:M0336:AthalianaCistrome_rc)	0.899	0.525	2.584	0.906	0.939	1	2	3	2	1	1.800	1	; oligos_7nt_mkv5_m1 versus AT3G49930.DAP_M0336_AthalianaCistrome_rc (AT3G49930.DAP:M0336:AthalianaCistrome_rc); m=1/4; ncol2=7; w=0; offset=2; strand=R; shift=2; score= 1.8; --wGATTTC--- ; cor=0.899; Ncor=0.525; logoDP=2.584; NsEucl=0.906; NSW=0.939; rcor=1; rNcor=2; rlogoDP=3; rNsEucl=2; rNSW=1; rank_mean=1.800; match_rank=1 a 0 0 46 0 96 0 0 0 0 0 0 0 c 0 0 12 0 6 0 0 0 102 0 0 0 g 0 0 14 102 0 0 0 0 0 0 0 0 t 0 0 30 0 0 102 102 102 0 0 0 0
AT5G22990.DAP_M0312_AthalianaCistrome_shift1 (AT5G22990.DAP:M0312:AthalianaCistrome)	0.760	0.522	4.145	0.909	0.909	3	3	1	1	2	2.000	2	; oligos_7nt_mkv5_m1 versus AT5G22990.DAP_M0312_AthalianaCistrome (AT5G22990.DAP:M0312:AthalianaCistrome); m=2/4; ncol2=15; w=0; offset=1; strand=D; shift=1; score= 2; -wCGwcwTCGwy ; cor=0.760; Ncor=0.522; logoDP=4.145; NsEucl=0.909; NSW=0.909; rcor=3; rNcor=3; rlogoDP=1; rNsEucl=1; rNSW=2; rank_mean=2.000; match_rank=2 a 0 169 0 32 220 133 249 44 0 17 232 81 c 0 79 571 2 13 269 3 51 584 4 25 187 g 0 10 0 528 28 41 108 2 0 547 20 41 t 0 326 13 22 323 141 224 487 0 16 307 275
APRR2_M1332_1.02_CISBP_rc_shift1 (APRR2:M1332_1.02:CISBP_rc)	0.767	0.639	1.269	0.903	0.906	2	1	4	3	3	2.600	3	; oligos_7nt_mkv5_m1 versus APRR2_M1332_1.02_CISBP_rc (APRR2:M1332_1.02:CISBP_rc); m=3/4; ncol2=10; w=0; offset=1; strand=R; shift=1; score= 2.6; -trGATtwysy- ; cor=0.767; Ncor=0.639; logoDP=1.269; NsEucl=0.903; NSW=0.906; rcor=2; rNcor=1; rlogoDP=4; rNsEucl=3; rNSW=3; rank_mean=2.600; match_rank=3 a 0 20 44 8 85 10 20 28 8 21 22 0 c 0 24 13 7 0 1 12 20 53 25 30 0 g 0 22 28 71 4 2 5 22 12 38 18 0 t 0 34 15 14 11 87 63 30 27 16 30 0
TIFY2A_M0760_1.02_CISBP_shift1 (TIFY2A:M0760_1.02:CISBP)	0.705	0.411	2.886	0.866	0.874	4	4	2	4	4	3.600	4	; oligos_7nt_mkv5_m1 versus TIFY2A_M0760_1.02_CISBP (TIFY2A:M0760_1.02:CISBP); m=4/4; ncol2=7; w=0; offset=1; strand=D; shift=1; score= 3.6; -haGATsd---- ; cor=0.705; Ncor=0.411; logoDP=2.886; NsEucl=0.866; NSW=0.874; rcor=4; rNcor=4; rlogoDP=2; rNsEucl=4; rNSW=4; rank_mean=3.600; match_rank=4 a 0 26 40 8 92 1 13 26 0 0 0 0 c 0 25 24 1 0 0 32 20 0 0 0 0 g 0 23 13 86 1 0 31 26 0 0 0 0 t 0 26 23 5 7 99 24 28 0 0 0 0