One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/07/compare-matrices_2019-07-07.133108_XSPJC6/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/2019/07/07/compare-matrices_2019-07-07.133108_XSPJC6/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift8 ; 28 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_5-8nt_m1_shift8 (oligos_5-8nt_m1)
; oligos_5-8nt_m1; m=0 (reference); ncol1=11; shift=8; ncol=19; --------hrAAACGrcra ; Alignment reference a 0 0 0 0 0 0 0 0 18 19 63 65 65 0 0 17 16 17 26 c 0 0 0 0 0 0 0 0 19 12 2 0 1 66 0 12 30 13 11 g 0 0 0 0 0 0 0 0 13 20 1 1 0 0 67 28 16 22 14 t 0 0 0 0 0 0 0 0 17 16 1 1 1 1 0 10 5 15 16

gw1.385.26.1_M0663_1.02_CISBP_shift8 (gw1.385.26.1:M0663_1.02:CISBP) 0.735 0.668 2.870 0.909 0.916 10 1 12 2 3 5.600 1
; oligos_5-8nt_m1 versus gw1.385.26.1_M0663_1.02_CISBP (gw1.385.26.1:M0663_1.02:CISBP); m=1/27; ncol2=10; w=10; offset=0; strand=D; shift=8; score= 5.6; --------vrwAAaGydm- ; cor=0.735; Ncor=0.668; logoDP=2.870; NsEucl=0.909; NSW=0.916; rcor=10; rNcor=1; rlogoDP=12; rNsEucl=2; rNSW=3; rank_mean=5.600; match_rank=1 a 0 0 0 0 0 0 0 0 25 34 46 83 86 64 6 15 26 28 0 c 0 0 0 0 0 0 0 0 26 19 9 7 6 22 3 27 17 26 0 g 0 0 0 0 0 0 0 0 26 25 13 2 0 5 86 21 31 23 0 t 0 0 0 0 0 0 0 0 23 22 32 8 8 9 5 37 26 23 0

PHYPADRAFT_38837_MA1022.1_JASPAR_shift8 (PHYPADRAFT_38837:MA1022.1:JASPAR) 0.732 0.666 2.838 0.908 0.916 12 2 13 3 4 6.800 2
; oligos_5-8nt_m1 versus PHYPADRAFT_38837_MA1022.1_JASPAR (PHYPADRAFT_38837:MA1022.1:JASPAR); m=2/27; ncol2=10; w=10; offset=0; strand=D; shift=8; score= 6.8; --------vrwAAaGydm- ; cor=0.732; Ncor=0.666; logoDP=2.838; NsEucl=0.908; NSW=0.916; rcor=12; rNcor=2; rlogoDP=13; rNsEucl=3; rNSW=4; rank_mean=6.800; match_rank=2 a 0 0 0 0 0 0 0 0 251 343 463 828 855 644 61 150 259 283 0 c 0 0 0 0 0 0 0 0 264 186 85 68 62 216 27 269 174 262 0 g 0 0 0 0 0 0 0 0 257 254 129 24 1 54 860 207 307 227 0 t 0 0 0 0 0 0 0 0 228 217 323 81 82 86 52 374 259 227 0

DOF1.8_MA0981.1_JASPAR_shift8 (DOF1.8:MA0981.1:JASPAR) 0.726 0.660 2.643 0.907 0.914 13 3 15 4 5 8.000 4
; oligos_5-8nt_m1 versus DOF1.8_MA0981.1_JASPAR (DOF1.8:MA0981.1:JASPAR); m=4/27; ncol2=10; w=10; offset=0; strand=D; shift=8; score= 8; --------vawAAaGtdr- ; cor=0.726; Ncor=0.660; logoDP=2.643; NsEucl=0.907; NSW=0.914; rcor=13; rNcor=3; rlogoDP=15; rNsEucl=4; rNSW=5; rank_mean=8.000; match_rank=4 a 0 0 0 0 0 0 0 0 251 321 415 812 831 658 65 170 268 288 0 c 0 0 0 0 0 0 0 0 259 197 100 72 64 233 23 241 189 209 0 g 0 0 0 0 0 0 0 0 256 250 135 38 3 27 846 231 270 269 0 t 0 0 0 0 0 0 0 0 234 233 350 77 102 83 65 359 273 234 0

AT1G64620_M0647_1.02_CISBP_shift8 (AT1G64620:M0647_1.02:CISBP) 0.724 0.658 2.689 0.907 0.914 14 4 14 5 6 8.600 7
; oligos_5-8nt_m1 versus AT1G64620_M0647_1.02_CISBP (AT1G64620:M0647_1.02:CISBP); m=7/27; ncol2=10; w=10; offset=0; strand=D; shift=8; score= 8.6; --------vrwAAaGtdr- ; cor=0.724; Ncor=0.658; logoDP=2.689; NsEucl=0.907; NSW=0.914; rcor=14; rNcor=4; rlogoDP=14; rNsEucl=5; rNSW=6; rank_mean=8.600; match_rank=7 a 0 0 0 0 0 0 0 0 25 32 41 81 84 66 7 17 27 29 0 c 0 0 0 0 0 0 0 0 26 20 10 7 6 23 2 24 19 21 0 g 0 0 0 0 0 0 0 0 26 25 14 4 0 3 85 23 27 27 0 t 0 0 0 0 0 0 0 0 23 23 35 8 10 8 6 36 27 23 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m1_shift8 (oligos_5-8nt_m1)													; oligos_5-8nt_m1; m=0 (reference); ncol1=11; shift=8; ncol=19; --------hrAAACGrcra ; Alignment reference a 0 0 0 0 0 0 0 0 18 19 63 65 65 0 0 17 16 17 26 c 0 0 0 0 0 0 0 0 19 12 2 0 1 66 0 12 30 13 11 g 0 0 0 0 0 0 0 0 13 20 1 1 0 0 67 28 16 22 14 t 0 0 0 0 0 0 0 0 17 16 1 1 1 1 0 10 5 15 16
gw1.385.26.1_M0663_1.02_CISBP_shift8 (gw1.385.26.1:M0663_1.02:CISBP)	0.735	0.668	2.870	0.909	0.916	10	1	12	2	3	5.600	1	; oligos_5-8nt_m1 versus gw1.385.26.1_M0663_1.02_CISBP (gw1.385.26.1:M0663_1.02:CISBP); m=1/27; ncol2=10; w=10; offset=0; strand=D; shift=8; score= 5.6; --------vrwAAaGydm- ; cor=0.735; Ncor=0.668; logoDP=2.870; NsEucl=0.909; NSW=0.916; rcor=10; rNcor=1; rlogoDP=12; rNsEucl=2; rNSW=3; rank_mean=5.600; match_rank=1 a 0 0 0 0 0 0 0 0 25 34 46 83 86 64 6 15 26 28 0 c 0 0 0 0 0 0 0 0 26 19 9 7 6 22 3 27 17 26 0 g 0 0 0 0 0 0 0 0 26 25 13 2 0 5 86 21 31 23 0 t 0 0 0 0 0 0 0 0 23 22 32 8 8 9 5 37 26 23 0
PHYPADRAFT_38837_MA1022.1_JASPAR_shift8 (PHYPADRAFT_38837:MA1022.1:JASPAR)	0.732	0.666	2.838	0.908	0.916	12	2	13	3	4	6.800	2	; oligos_5-8nt_m1 versus PHYPADRAFT_38837_MA1022.1_JASPAR (PHYPADRAFT_38837:MA1022.1:JASPAR); m=2/27; ncol2=10; w=10; offset=0; strand=D; shift=8; score= 6.8; --------vrwAAaGydm- ; cor=0.732; Ncor=0.666; logoDP=2.838; NsEucl=0.908; NSW=0.916; rcor=12; rNcor=2; rlogoDP=13; rNsEucl=3; rNSW=4; rank_mean=6.800; match_rank=2 a 0 0 0 0 0 0 0 0 251 343 463 828 855 644 61 150 259 283 0 c 0 0 0 0 0 0 0 0 264 186 85 68 62 216 27 269 174 262 0 g 0 0 0 0 0 0 0 0 257 254 129 24 1 54 860 207 307 227 0 t 0 0 0 0 0 0 0 0 228 217 323 81 82 86 52 374 259 227 0
DOF1.8_MA0981.1_JASPAR_shift8 (DOF1.8:MA0981.1:JASPAR)	0.726	0.660	2.643	0.907	0.914	13	3	15	4	5	8.000	4	; oligos_5-8nt_m1 versus DOF1.8_MA0981.1_JASPAR (DOF1.8:MA0981.1:JASPAR); m=4/27; ncol2=10; w=10; offset=0; strand=D; shift=8; score= 8; --------vawAAaGtdr- ; cor=0.726; Ncor=0.660; logoDP=2.643; NsEucl=0.907; NSW=0.914; rcor=13; rNcor=3; rlogoDP=15; rNsEucl=4; rNSW=5; rank_mean=8.000; match_rank=4 a 0 0 0 0 0 0 0 0 251 321 415 812 831 658 65 170 268 288 0 c 0 0 0 0 0 0 0 0 259 197 100 72 64 233 23 241 189 209 0 g 0 0 0 0 0 0 0 0 256 250 135 38 3 27 846 231 270 269 0 t 0 0 0 0 0 0 0 0 234 233 350 77 102 83 65 359 273 234 0
AT1G64620_M0647_1.02_CISBP_shift8 (AT1G64620:M0647_1.02:CISBP)	0.724	0.658	2.689	0.907	0.914	14	4	14	5	6	8.600	7	; oligos_5-8nt_m1 versus AT1G64620_M0647_1.02_CISBP (AT1G64620:M0647_1.02:CISBP); m=7/27; ncol2=10; w=10; offset=0; strand=D; shift=8; score= 8.6; --------vrwAAaGtdr- ; cor=0.724; Ncor=0.658; logoDP=2.689; NsEucl=0.907; NSW=0.914; rcor=14; rNcor=4; rlogoDP=14; rNsEucl=5; rNSW=6; rank_mean=8.600; match_rank=7 a 0 0 0 0 0 0 0 0 25 32 41 81 84 66 7 17 27 29 0 c 0 0 0 0 0 0 0 0 26 20 10 7 6 23 2 24 19 21 0 g 0 0 0 0 0 0 0 0 26 25 14 4 0 3 85 23 27 27 0 t 0 0 0 0 0 0 0 0 23 23 35 8 10 8 6 36 27 23 0