One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151802_2ev0Km/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/2026/05/29/compare-matrices_2026-05-29.151802_2ev0Km/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift2 ; 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_test_vs_ctrl_m1_shift2 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=19; shift=2; ncol=21; --gmkGCATGwrwcakGCCkw ; Alignment reference a 0 0 5 6 4 0 1 19 2 2 9 6 7 4 14 2 0 0 0 4 8 c 0 0 3 8 1 0 19 1 3 1 2 4 3 14 0 3 0 21 21 3 2 g 0 0 8 2 8 20 1 0 1 17 4 7 4 0 4 8 21 0 0 7 1 t 0 0 5 5 8 1 0 1 15 1 6 4 7 3 3 8 0 0 0 7 10

LEC2_MA0581.1_JASPAR_rc_shift1 (LEC2:MA0581.1:JASPAR_rc) 0.878 0.439 0.350 0.931 0.952 1 4 4 1 1 2.200 1
; dyads_test_vs_ctrl_m1 versus LEC2_MA0581.1_JASPAR_rc (LEC2:MA0581.1:JASPAR_rc); m=1/5; ncol2=11; w=-1; offset=-1; strand=R; shift=1; score= 2.2; -awgyGCATGsa--------- ; cor=0.878; Ncor=0.439; logoDP=0.350; NsEucl=0.931; NSW=0.952; rcor=1; rNcor=4; rlogoDP=4; rNsEucl=1; rNSW=1; rank_mean=2.200; match_rank=1 a 0 250 129 94 0 0 0 487 0 10 63 175 0 0 0 0 0 0 0 0 0 c 0 62 44 60 156 0 487 0 0 0 165 119 0 0 0 0 0 0 0 0 0 g 0 79 86 218 30 487 0 0 0 475 163 86 0 0 0 0 0 0 0 0 0 t 0 96 228 115 301 0 0 0 487 2 96 107 0 0 0 0 0 0 0 0 0

AtLEC2_AtLEC2_Athamap_rc_shift2 (AtLEC2:AtLEC2:Athamap_rc) 0.851 0.448 0.235 0.914 0.926 2 2 5 3 2 2.800 2
; dyads_test_vs_ctrl_m1 versus AtLEC2_AtLEC2_Athamap_rc (AtLEC2:AtLEC2:Athamap_rc); m=2/5; ncol2=10; w=0; offset=0; strand=R; shift=2; score= 2.8; --ttTGCATGrm--------- ; cor=0.851; Ncor=0.448; logoDP=0.235; NsEucl=0.914; NSW=0.926; rcor=2; rNcor=2; rlogoDP=5; rNsEucl=3; rNSW=2; rank_mean=2.800; match_rank=2 a 0 0 1 1 0 0 0 9 0 0 3 4 0 0 0 0 0 0 0 0 0 c 0 0 1 1 0 0 9 0 0 0 0 3 0 0 0 0 0 0 0 0 0 g 0 0 1 1 0 9 0 0 0 9 4 0 0 0 0 0 0 0 0 0 0 t 0 0 5 5 9 0 0 0 9 0 2 2 0 0 0 0 0 0 0 0 0

FUS3.DAP_M0003_AthalianaCistrome_rc_shift0 (FUS3.DAP:M0003:AthalianaCistrome_rc) 0.741 0.459 0.378 0.916 0.907 4 1 3 2 4 2.800 3
; dyads_test_vs_ctrl_m1 versus FUS3.DAP_M0003_AthalianaCistrome_rc (FUS3.DAP:M0003:AthalianaCistrome_rc); m=3/5; ncol2=15; w=-2; offset=-2; strand=R; shift=0; score= 2.8; trywTGCATGyatdt------ ; cor=0.741; Ncor=0.459; logoDP=0.378; NsEucl=0.916; NSW=0.907; rcor=4; rNcor=1; rlogoDP=3; rNsEucl=2; rNSW=4; rank_mean=2.800; match_rank=3 a 120 155 95 330 0 0 0 589 0 0 38 348 106 210 132 0 0 0 0 0 0 c 77 77 229 23 1 0 585 0 0 0 230 33 94 63 62 0 0 0 0 0 0 g 63 222 58 30 0 589 1 0 0 589 50 118 47 155 76 0 0 0 0 0 0 t 329 135 207 206 588 0 3 0 589 0 271 90 342 161 319 0 0 0 0 0 0

FUS3_MA0565.2_JASPAR_rc_shift3 (FUS3:MA0565.2:JASPAR_rc) 0.849 0.447 3.776 0.912 0.923 3 3 2 4 3 3.000 4
; dyads_test_vs_ctrl_m1 versus FUS3_MA0565.2_JASPAR_rc (FUS3:MA0565.2:JASPAR_rc); m=4/5; ncol2=10; w=0; offset=1; strand=R; shift=3; score= 3; ---wTGCATGTdw-------- ; cor=0.849; Ncor=0.447; logoDP=3.776; NsEucl=0.912; NSW=0.923; rcor=3; rNcor=3; rlogoDP=2; rNsEucl=4; rNSW=3; rank_mean=3.000; match_rank=4 a 0 0 0 477 45 0 0 1137 1 0 0 339 307 0 0 0 0 0 0 0 0 c 0 0 0 98 28 0 1145 1 2 0 0 143 218 0 0 0 0 0 0 0 0 g 0 0 0 125 18 1146 1 5 2 1146 0 309 152 0 0 0 0 0 0 0 0 t 0 0 0 446 1055 0 0 3 1141 0 1146 355 469 0 0 0 0 0 0 0 0

ABI19_B73_1_m1_EEAD0171_EEADannot_shift2 (ABI19_B73_1_m1:EEAD0171:EEADannot) 0.728 0.421 5.250 0.892 0.873 5 5 1 5 5 4.200 5
; dyads_test_vs_ctrl_m1 versus ABI19_B73_1_m1_EEAD0171_EEADannot (ABI19_B73_1_m1:EEAD0171:EEADannot); m=5/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 4.2; --CwTGCATGCry-------- ; cor=0.728; Ncor=0.421; logoDP=5.250; NsEucl=0.892; NSW=0.873; rcor=5; rNcor=5; rlogoDP=1; rNsEucl=5; rNSW=5; rank_mean=4.200; match_rank=5 a 0 0 2 62 1 0 0 99 0 0 2 65 7 0 0 0 0 0 0 0 0 c 0 0 85 3 2 1 100 0 3 1 90 2 31 0 0 0 0 0 0 0 0 g 0 0 6 2 0 99 0 0 1 99 2 32 20 0 0 0 0 0 0 0 0 t 0 0 7 33 97 0 0 1 96 0 6 1 42 0 0 0 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m1_shift2 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=19; shift=2; ncol=21; --gmkGCATGwrwcakGCCkw ; Alignment reference a 0 0 5 6 4 0 1 19 2 2 9 6 7 4 14 2 0 0 0 4 8 c 0 0 3 8 1 0 19 1 3 1 2 4 3 14 0 3 0 21 21 3 2 g 0 0 8 2 8 20 1 0 1 17 4 7 4 0 4 8 21 0 0 7 1 t 0 0 5 5 8 1 0 1 15 1 6 4 7 3 3 8 0 0 0 7 10
LEC2_MA0581.1_JASPAR_rc_shift1 (LEC2:MA0581.1:JASPAR_rc)	0.878	0.439	0.350	0.931	0.952	1	4	4	1	1	2.200	1	; dyads_test_vs_ctrl_m1 versus LEC2_MA0581.1_JASPAR_rc (LEC2:MA0581.1:JASPAR_rc); m=1/5; ncol2=11; w=-1; offset=-1; strand=R; shift=1; score= 2.2; -awgyGCATGsa--------- ; cor=0.878; Ncor=0.439; logoDP=0.350; NsEucl=0.931; NSW=0.952; rcor=1; rNcor=4; rlogoDP=4; rNsEucl=1; rNSW=1; rank_mean=2.200; match_rank=1 a 0 250 129 94 0 0 0 487 0 10 63 175 0 0 0 0 0 0 0 0 0 c 0 62 44 60 156 0 487 0 0 0 165 119 0 0 0 0 0 0 0 0 0 g 0 79 86 218 30 487 0 0 0 475 163 86 0 0 0 0 0 0 0 0 0 t 0 96 228 115 301 0 0 0 487 2 96 107 0 0 0 0 0 0 0 0 0
AtLEC2_AtLEC2_Athamap_rc_shift2 (AtLEC2:AtLEC2:Athamap_rc)	0.851	0.448	0.235	0.914	0.926	2	2	5	3	2	2.800	2	; dyads_test_vs_ctrl_m1 versus AtLEC2_AtLEC2_Athamap_rc (AtLEC2:AtLEC2:Athamap_rc); m=2/5; ncol2=10; w=0; offset=0; strand=R; shift=2; score= 2.8; --ttTGCATGrm--------- ; cor=0.851; Ncor=0.448; logoDP=0.235; NsEucl=0.914; NSW=0.926; rcor=2; rNcor=2; rlogoDP=5; rNsEucl=3; rNSW=2; rank_mean=2.800; match_rank=2 a 0 0 1 1 0 0 0 9 0 0 3 4 0 0 0 0 0 0 0 0 0 c 0 0 1 1 0 0 9 0 0 0 0 3 0 0 0 0 0 0 0 0 0 g 0 0 1 1 0 9 0 0 0 9 4 0 0 0 0 0 0 0 0 0 0 t 0 0 5 5 9 0 0 0 9 0 2 2 0 0 0 0 0 0 0 0 0
FUS3.DAP_M0003_AthalianaCistrome_rc_shift0 (FUS3.DAP:M0003:AthalianaCistrome_rc)	0.741	0.459	0.378	0.916	0.907	4	1	3	2	4	2.800	3	; dyads_test_vs_ctrl_m1 versus FUS3.DAP_M0003_AthalianaCistrome_rc (FUS3.DAP:M0003:AthalianaCistrome_rc); m=3/5; ncol2=15; w=-2; offset=-2; strand=R; shift=0; score= 2.8; trywTGCATGyatdt------ ; cor=0.741; Ncor=0.459; logoDP=0.378; NsEucl=0.916; NSW=0.907; rcor=4; rNcor=1; rlogoDP=3; rNsEucl=2; rNSW=4; rank_mean=2.800; match_rank=3 a 120 155 95 330 0 0 0 589 0 0 38 348 106 210 132 0 0 0 0 0 0 c 77 77 229 23 1 0 585 0 0 0 230 33 94 63 62 0 0 0 0 0 0 g 63 222 58 30 0 589 1 0 0 589 50 118 47 155 76 0 0 0 0 0 0 t 329 135 207 206 588 0 3 0 589 0 271 90 342 161 319 0 0 0 0 0 0
FUS3_MA0565.2_JASPAR_rc_shift3 (FUS3:MA0565.2:JASPAR_rc)	0.849	0.447	3.776	0.912	0.923	3	3	2	4	3	3.000	4	; dyads_test_vs_ctrl_m1 versus FUS3_MA0565.2_JASPAR_rc (FUS3:MA0565.2:JASPAR_rc); m=4/5; ncol2=10; w=0; offset=1; strand=R; shift=3; score= 3; ---wTGCATGTdw-------- ; cor=0.849; Ncor=0.447; logoDP=3.776; NsEucl=0.912; NSW=0.923; rcor=3; rNcor=3; rlogoDP=2; rNsEucl=4; rNSW=3; rank_mean=3.000; match_rank=4 a 0 0 0 477 45 0 0 1137 1 0 0 339 307 0 0 0 0 0 0 0 0 c 0 0 0 98 28 0 1145 1 2 0 0 143 218 0 0 0 0 0 0 0 0 g 0 0 0 125 18 1146 1 5 2 1146 0 309 152 0 0 0 0 0 0 0 0 t 0 0 0 446 1055 0 0 3 1141 0 1146 355 469 0 0 0 0 0 0 0 0
ABI19_B73_1_m1_EEAD0171_EEADannot_shift2 (ABI19_B73_1_m1:EEAD0171:EEADannot)	0.728	0.421	5.250	0.892	0.873	5	5	1	5	5	4.200	5	; dyads_test_vs_ctrl_m1 versus ABI19_B73_1_m1_EEAD0171_EEADannot (ABI19_B73_1_m1:EEAD0171:EEADannot); m=5/5; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 4.2; --CwTGCATGCry-------- ; cor=0.728; Ncor=0.421; logoDP=5.250; NsEucl=0.892; NSW=0.873; rcor=5; rNcor=5; rlogoDP=1; rNsEucl=5; rNSW=5; rank_mean=4.200; match_rank=5 a 0 0 2 62 1 0 0 99 0 0 2 65 7 0 0 0 0 0 0 0 0 c 0 0 85 3 2 1 100 0 3 1 90 2 31 0 0 0 0 0 0 0 0 g 0 0 6 2 0 99 0 0 1 99 2 32 20 0 0 0 0 0 0 0 0 t 0 0 7 33 97 0 0 1 96 0 6 1 42 0 0 0 0 0 0 0 0