One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/09/18/compare-matrices_2025-09-18.145524_EpIP5Q/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/2025/09/18/compare-matrices_2025-09-18.145524_EpIP5Q/compare-matrices.tab

One-to-n matrix alignment; reference matrix: assembly_15_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
assembly_15_shift0 (assembly_1)
; assembly_15 (assembly_1); m=0 (reference); ncol1=40; shift=0; ncol=40; wwGACAGAAaaragAsAGAGAGAsarwdGcAGAGAGAcww ; Alignment reference a 990 1150 260 2523 419 2544 399 2568 2486 1176 1117 275 483 207 711 129 899 64 920 36 910 53 759 233 450 298 218 157 77 98 462 52 475 31 472 55 443 72 195 184 c 392 333 96 46 1884 32 121 36 48 387 477 124 106 86 43 472 11 25 5 20 8 37 39 258 105 142 55 72 17 299 7 14 5 12 3 22 15 290 69 86 g 537 400 2162 37 245 34 2018 31 80 489 437 320 134 516 96 271 17 826 10 863 11 824 58 305 172 290 83 125 355 61 11 406 7 432 9 398 16 78 89 97 t 763 799 164 76 134 72 144 47 68 630 651 225 221 135 94 72 17 29 9 25 15 30 88 148 217 214 141 143 48 39 17 25 10 22 13 22 23 57 144 130

BPC1_MA1404.1_JASPAR_shift13 (BPC1:MA1404.1:JASPAR) 0.798 0.479 11.003 0.937 0.903 1 3 2 2 2 2.000 1
; assembly_15 versus BPC1_MA1404.1_JASPAR (BPC1:MA1404.1:JASPAR); m=1/5; ncol2=24; w=0; offset=13; strand=D; shift=13; score= 2; -------------GAGAGAGAGAGAGAGAGAGAGAGA--- ; cor=0.798; Ncor=0.479; logoDP=11.003; NsEucl=0.937; NSW=0.903; rcor=1; rNcor=3; rlogoDP=2; rNsEucl=2; rNSW=2; rank_mean=2.000; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 0 0 0 82 483 8 501 67 500 43 478 39 520 27 518 62 460 54 485 41 508 71 478 73 450 47 436 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 18 4 15 0 9 0 17 3 0 6 2 11 9 0 0 0 10 0 2 12 19 15 20 22 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 421 29 483 18 448 39 461 44 482 2 508 3 450 56 462 54 467 9 459 35 440 39 427 43 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 18 23 33 20 15 0 18 14 18 11 2 7 18 23 23 0 21 22 7 14 7 35 45 38 0 0 0

BPC5.ampDAP_M0153_AthalianaCistrome_shift9 (BPC5.ampDAP:M0153:AthalianaCistrome) 0.741 0.537 9.943 0.942 0.903 5 2 3 1 3 2.800 2
; assembly_15 versus BPC5.ampDAP_M0153_AthalianaCistrome (BPC5.ampDAP:M0153:AthalianaCistrome); m=2/5; ncol2=29; w=0; offset=9; strand=D; shift=9; score= 2.8; ---------rrrararaGAGARAGAGAGAGAGAGAGAG-- ; cor=0.741; Ncor=0.537; logoDP=9.943; NsEucl=0.942; NSW=0.903; rcor=5; rNcor=2; rlogoDP=3; rNsEucl=1; rNSW=3; rank_mean=2.800; match_rank=2 a 0 0 0 0 0 0 0 0 0 19 33 14 30 14 28 17 33 9 40 2 36 13 37 3 41 6 47 9 46 7 49 4 43 8 48 3 50 4 0 0 c 0 0 0 0 0 0 0 0 0 5 3 5 6 7 7 0 3 2 0 2 5 0 2 1 0 0 0 0 0 1 0 0 1 0 0 0 0 3 0 0 g 0 0 0 0 0 0 0 0 0 22 14 27 12 25 8 26 12 39 0 41 7 36 9 42 3 44 3 40 4 42 0 45 6 40 2 47 0 42 0 0 t 0 0 0 0 0 0 0 0 0 4 0 4 2 4 7 7 2 0 10 5 2 1 2 4 6 0 0 1 0 0 1 1 0 2 0 0 0 1 0 0

FRS9.DAP_M0713_AthalianaCistrome_rc_shift11 (FRS9.DAP:M0713:AthalianaCistrome_rc) 0.773 0.406 0.807 0.932 0.904 2 4 5 3 1 3.000 3
; assembly_15 versus FRS9.DAP_M0713_AthalianaCistrome_rc (FRS9.DAP:M0713:AthalianaCistrome_rc); m=3/5; ncol2=21; w=0; offset=11; strand=R; shift=11; score= 3; -----------GAGAGAGAGAGAGAGAGAGAG-------- ; cor=0.773; Ncor=0.406; logoDP=0.807; NsEucl=0.932; NSW=0.904; rcor=2; rNcor=4; rlogoDP=5; rNsEucl=3; rNSW=1; rank_mean=3.000; match_rank=3 a 0 0 0 0 0 0 0 0 0 0 0 119 454 74 428 123 509 0 566 46 570 37 558 28 511 126 493 57 453 82 455 94 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 10 18 13 13 21 0 8 0 0 0 0 0 0 1 7 11 42 0 10 8 10 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 404 69 436 117 393 48 567 7 527 1 522 14 531 35 426 46 453 48 431 72 402 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 42 34 52 17 38 18 0 2 2 4 16 3 16 28 16 25 23 74 52 40 69 0 0 0 0 0 0 0 0

BPC5_MA1403.1_JASPAR_shift8 (BPC5:MA1403.1:JASPAR) 0.749 0.562 17.852 0.928 0.846 4 1 1 4 5 3.000 4
; assembly_15 versus BPC5_MA1403.1_JASPAR (BPC5:MA1403.1:JASPAR); m=4/5; ncol2=30; w=0; offset=8; strand=D; shift=8; score= 3; --------AGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-- ; cor=0.749; Ncor=0.562; logoDP=17.852; NsEucl=0.928; NSW=0.846; rcor=4; rNcor=1; rlogoDP=1; rNsEucl=4; rNSW=5; rank_mean=3.000; match_rank=4 a 0 0 0 0 0 0 0 0 95 3 102 2 100 1 99 0 99 1 102 0 102 4 101 2 101 1 98 1 101 0 100 1 98 1 98 0 100 5 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 1 0 1 0 1 0 1 0 1 0 4 2 3 0 0 g 0 0 0 0 0 0 0 0 7 99 0 98 0 99 0 100 2 100 0 102 0 97 1 100 1 100 1 99 1 101 0 99 3 99 0 98 0 91 0 0 t 0 0 0 0 0 0 0 0 0 0 0 2 2 2 3 1 1 0 0 0 0 1 0 0 0 0 3 1 0 0 2 1 1 1 4 0 0 3 0 0

BPC6_MA1402.1_JASPAR_rc_shift13 (BPC6:MA1402.1:JASPAR_rc) 0.763 0.401 1.042 0.925 0.882 3 5 4 5 4 4.200 5
; assembly_15 versus BPC6_MA1402.1_JASPAR_rc (BPC6:MA1402.1:JASPAR_rc); m=5/5; ncol2=21; w=0; offset=13; strand=R; shift=13; score= 4.2; -------------kAGAGAGAGAGAGAGAGAGAG------ ; cor=0.763; Ncor=0.401; logoDP=1.042; NsEucl=0.925; NSW=0.882; rcor=3; rNcor=5; rlogoDP=4; rNsEucl=5; rNSW=4; rank_mean=4.200; match_rank=5 a 0 0 0 0 0 0 0 0 0 0 0 0 0 14 181 12 174 3 181 7 187 0 186 19 187 8 179 25 175 27 161 4 151 28 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 5 0 0 0 0 0 0 0 2 1 3 5 7 5 10 0 2 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 123 2 170 6 168 3 169 1 186 0 168 1 177 6 160 2 142 7 161 19 134 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 50 3 6 8 12 4 12 0 2 2 1 0 1 2 0 6 12 15 13 18 24 0 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
assembly_15_shift0 (assembly_1)													; assembly_15 (assembly_1); m=0 (reference); ncol1=40; shift=0; ncol=40; wwGACAGAAaaragAsAGAGAGAsarwdGcAGAGAGAcww ; Alignment reference a 990 1150 260 2523 419 2544 399 2568 2486 1176 1117 275 483 207 711 129 899 64 920 36 910 53 759 233 450 298 218 157 77 98 462 52 475 31 472 55 443 72 195 184 c 392 333 96 46 1884 32 121 36 48 387 477 124 106 86 43 472 11 25 5 20 8 37 39 258 105 142 55 72 17 299 7 14 5 12 3 22 15 290 69 86 g 537 400 2162 37 245 34 2018 31 80 489 437 320 134 516 96 271 17 826 10 863 11 824 58 305 172 290 83 125 355 61 11 406 7 432 9 398 16 78 89 97 t 763 799 164 76 134 72 144 47 68 630 651 225 221 135 94 72 17 29 9 25 15 30 88 148 217 214 141 143 48 39 17 25 10 22 13 22 23 57 144 130
BPC1_MA1404.1_JASPAR_shift13 (BPC1:MA1404.1:JASPAR)	0.798	0.479	11.003	0.937	0.903	1	3	2	2	2	2.000	1	; assembly_15 versus BPC1_MA1404.1_JASPAR (BPC1:MA1404.1:JASPAR); m=1/5; ncol2=24; w=0; offset=13; strand=D; shift=13; score= 2; -------------GAGAGAGAGAGAGAGAGAGAGAGA--- ; cor=0.798; Ncor=0.479; logoDP=11.003; NsEucl=0.937; NSW=0.903; rcor=1; rNcor=3; rlogoDP=2; rNsEucl=2; rNSW=2; rank_mean=2.000; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 0 0 0 82 483 8 501 67 500 43 478 39 520 27 518 62 460 54 485 41 508 71 478 73 450 47 436 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 18 4 15 0 9 0 17 3 0 6 2 11 9 0 0 0 10 0 2 12 19 15 20 22 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 421 29 483 18 448 39 461 44 482 2 508 3 450 56 462 54 467 9 459 35 440 39 427 43 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 18 23 33 20 15 0 18 14 18 11 2 7 18 23 23 0 21 22 7 14 7 35 45 38 0 0 0
BPC5.ampDAP_M0153_AthalianaCistrome_shift9 (BPC5.ampDAP:M0153:AthalianaCistrome)	0.741	0.537	9.943	0.942	0.903	5	2	3	1	3	2.800	2	; assembly_15 versus BPC5.ampDAP_M0153_AthalianaCistrome (BPC5.ampDAP:M0153:AthalianaCistrome); m=2/5; ncol2=29; w=0; offset=9; strand=D; shift=9; score= 2.8; ---------rrrararaGAGARAGAGAGAGAGAGAGAG-- ; cor=0.741; Ncor=0.537; logoDP=9.943; NsEucl=0.942; NSW=0.903; rcor=5; rNcor=2; rlogoDP=3; rNsEucl=1; rNSW=3; rank_mean=2.800; match_rank=2 a 0 0 0 0 0 0 0 0 0 19 33 14 30 14 28 17 33 9 40 2 36 13 37 3 41 6 47 9 46 7 49 4 43 8 48 3 50 4 0 0 c 0 0 0 0 0 0 0 0 0 5 3 5 6 7 7 0 3 2 0 2 5 0 2 1 0 0 0 0 0 1 0 0 1 0 0 0 0 3 0 0 g 0 0 0 0 0 0 0 0 0 22 14 27 12 25 8 26 12 39 0 41 7 36 9 42 3 44 3 40 4 42 0 45 6 40 2 47 0 42 0 0 t 0 0 0 0 0 0 0 0 0 4 0 4 2 4 7 7 2 0 10 5 2 1 2 4 6 0 0 1 0 0 1 1 0 2 0 0 0 1 0 0
FRS9.DAP_M0713_AthalianaCistrome_rc_shift11 (FRS9.DAP:M0713:AthalianaCistrome_rc)	0.773	0.406	0.807	0.932	0.904	2	4	5	3	1	3.000	3	; assembly_15 versus FRS9.DAP_M0713_AthalianaCistrome_rc (FRS9.DAP:M0713:AthalianaCistrome_rc); m=3/5; ncol2=21; w=0; offset=11; strand=R; shift=11; score= 3; -----------GAGAGAGAGAGAGAGAGAGAG-------- ; cor=0.773; Ncor=0.406; logoDP=0.807; NsEucl=0.932; NSW=0.904; rcor=2; rNcor=4; rlogoDP=5; rNsEucl=3; rNSW=1; rank_mean=3.000; match_rank=3 a 0 0 0 0 0 0 0 0 0 0 0 119 454 74 428 123 509 0 566 46 570 37 558 28 511 126 493 57 453 82 455 94 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 10 18 13 13 21 0 8 0 0 0 0 0 0 1 7 11 42 0 10 8 10 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 404 69 436 117 393 48 567 7 527 1 522 14 531 35 426 46 453 48 431 72 402 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 42 34 52 17 38 18 0 2 2 4 16 3 16 28 16 25 23 74 52 40 69 0 0 0 0 0 0 0 0
BPC5_MA1403.1_JASPAR_shift8 (BPC5:MA1403.1:JASPAR)	0.749	0.562	17.852	0.928	0.846	4	1	1	4	5	3.000	4	; assembly_15 versus BPC5_MA1403.1_JASPAR (BPC5:MA1403.1:JASPAR); m=4/5; ncol2=30; w=0; offset=8; strand=D; shift=8; score= 3; --------AGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-- ; cor=0.749; Ncor=0.562; logoDP=17.852; NsEucl=0.928; NSW=0.846; rcor=4; rNcor=1; rlogoDP=1; rNsEucl=4; rNSW=5; rank_mean=3.000; match_rank=4 a 0 0 0 0 0 0 0 0 95 3 102 2 100 1 99 0 99 1 102 0 102 4 101 2 101 1 98 1 101 0 100 1 98 1 98 0 100 5 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 1 0 1 0 1 0 1 0 1 0 4 2 3 0 0 g 0 0 0 0 0 0 0 0 7 99 0 98 0 99 0 100 2 100 0 102 0 97 1 100 1 100 1 99 1 101 0 99 3 99 0 98 0 91 0 0 t 0 0 0 0 0 0 0 0 0 0 0 2 2 2 3 1 1 0 0 0 0 1 0 0 0 0 3 1 0 0 2 1 1 1 4 0 0 3 0 0
BPC6_MA1402.1_JASPAR_rc_shift13 (BPC6:MA1402.1:JASPAR_rc)	0.763	0.401	1.042	0.925	0.882	3	5	4	5	4	4.200	5	; assembly_15 versus BPC6_MA1402.1_JASPAR_rc (BPC6:MA1402.1:JASPAR_rc); m=5/5; ncol2=21; w=0; offset=13; strand=R; shift=13; score= 4.2; -------------kAGAGAGAGAGAGAGAGAGAG------ ; cor=0.763; Ncor=0.401; logoDP=1.042; NsEucl=0.925; NSW=0.882; rcor=3; rNcor=5; rlogoDP=4; rNsEucl=5; rNSW=4; rank_mean=4.200; match_rank=5 a 0 0 0 0 0 0 0 0 0 0 0 0 0 14 181 12 174 3 181 7 187 0 186 19 187 8 179 25 175 27 161 4 151 28 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 5 0 0 0 0 0 0 0 2 1 3 5 7 5 10 0 2 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 123 2 170 6 168 3 169 1 186 0 168 1 177 6 160 2 142 7 161 19 134 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 50 3 6 8 12 4 12 0 2 2 1 0 1 2 0 6 12 15 13 18 24 0 0 0 0 0 0