One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.132020_hsVPCK/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/2019/07/04/compare-matrices_2019-07-04.132020_hsVPCK/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift3 ; 23 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_shift3 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=10; shift=3; ncol=16; ---whGTCGACdw--- ; Alignment reference a 0 0 0 226 188 36 72 37 6 550 20 193 214 0 0 0 c 0 0 0 134 224 21 75 640 11 20 618 100 131 0 0 0 g 0 0 0 125 95 629 20 18 656 63 24 217 132 0 0 0 t 0 0 0 220 198 19 538 10 32 72 43 195 228 0 0 0

ETT_ETT_2_ArabidopsisPBM_shift3 (ETT:ETT_2:ArabidopsisPBM) 0.880 0.880 3.965 0.931 0.953 1 1 8 1 1 2.400 1
; dyads_test_vs_ctrl_m1 versus ETT_ETT_2_ArabidopsisPBM (ETT:ETT_2:ArabidopsisPBM); m=1/22; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 2.4; ---htGTCGACag--- ; cor=0.880; Ncor=0.880; logoDP=3.965; NsEucl=0.931; NSW=0.953; rcor=1; rNcor=1; rlogoDP=8; rNsEucl=1; rNSW=1; rank_mean=2.400; match_rank=1 a 0 0 0 25 5 7 3 9 1 93 1 66 8 0 0 0 c 0 0 0 28 6 2 1 88 2 3 90 23 6 0 0 0 g 0 0 0 11 23 90 3 2 88 1 2 6 66 0 0 0 t 0 0 0 36 66 1 93 1 9 3 7 5 20 0 0 0

DREB1G_MA1032.1_JASPAR_shift3 (DREB1G:MA1032.1:JASPAR) 0.747 0.747 4.900 0.898 0.896 10 2 1 10 10 6.600 3
; dyads_test_vs_ctrl_m1 versus DREB1G_MA1032.1_JASPAR (DREB1G:MA1032.1:JASPAR); m=3/22; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 6.6; ---atGCCGACAt--- ; cor=0.747; Ncor=0.747; logoDP=4.900; NsEucl=0.898; NSW=0.896; rcor=10; rNcor=2; rlogoDP=1; rNsEucl=10; rNSW=10; rank_mean=6.600; match_rank=3 a 0 0 0 314 119 180 0 0 0 884 0 845 131 0 0 0 c 0 0 0 229 226 0 999 999 0 0 999 22 219 0 0 0 g 0 0 0 229 119 820 0 0 999 115 0 22 221 0 0 0 t 0 0 0 229 535 0 0 0 0 0 0 111 430 0 0 0

DREB1A_MA0971.1_JASPAR_rc_shift3 (DREB1A:MA0971.1:JASPAR_rc) 0.737 0.737 4.529 0.901 0.903 12 4 7 6 7 7.200 4
; dyads_test_vs_ctrl_m1 versus DREB1A_MA0971.1_JASPAR_rc (DREB1A:MA0971.1:JASPAR_rc); m=4/22; ncol2=10; w=10; offset=0; strand=R; shift=3; score= 7.2; ---yyrCCGACat--- ; cor=0.737; Ncor=0.737; logoDP=4.529; NsEucl=0.901; NSW=0.903; rcor=12; rNcor=4; rlogoDP=7; rNsEucl=6; rNSW=7; rank_mean=7.200; match_rank=4 a 0 0 0 152 140 461 3 6 1 973 1 565 166 0 0 0 c 0 0 0 322 279 19 948 994 4 3 997 137 126 0 0 0 g 0 0 0 205 240 504 0 0 991 14 0 159 118 0 0 0 t 0 0 0 322 341 16 48 0 5 10 2 139 590 0 0 0

LOC_Os02g45450_M0042_1.02_CISBP_shift3 (LOC_Os02g45450:M0042_1.02:CISBP) 0.746 0.746 4.893 0.898 0.896 11 3 2 11 11 7.600 6
; dyads_test_vs_ctrl_m1 versus LOC_Os02g45450_M0042_1.02_CISBP (LOC_Os02g45450:M0042_1.02:CISBP); m=6/22; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 7.6; ---atGCCGACAt--- ; cor=0.746; Ncor=0.746; logoDP=4.893; NsEucl=0.898; NSW=0.896; rcor=11; rNcor=3; rlogoDP=2; rNsEucl=11; rNSW=11; rank_mean=7.600; match_rank=6 a 0 0 0 31 12 18 0 0 0 88 0 85 13 0 0 0 c 0 0 0 23 23 0 100 100 0 0 100 2 22 0 0 0 g 0 0 0 23 12 82 0 0 100 12 0 2 22 0 0 0 t 0 0 0 23 53 0 0 0 0 0 0 11 43 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_shift3 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=10; shift=3; ncol=16; ---whGTCGACdw--- ; Alignment reference a 0 0 0 226 188 36 72 37 6 550 20 193 214 0 0 0 c 0 0 0 134 224 21 75 640 11 20 618 100 131 0 0 0 g 0 0 0 125 95 629 20 18 656 63 24 217 132 0 0 0 t 0 0 0 220 198 19 538 10 32 72 43 195 228 0 0 0
ETT_ETT_2_ArabidopsisPBM_shift3 (ETT:ETT_2:ArabidopsisPBM)	0.880	0.880	3.965	0.931	0.953	1	1	8	1	1	2.400	1	; dyads_test_vs_ctrl_m1 versus ETT_ETT_2_ArabidopsisPBM (ETT:ETT_2:ArabidopsisPBM); m=1/22; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 2.4; ---htGTCGACag--- ; cor=0.880; Ncor=0.880; logoDP=3.965; NsEucl=0.931; NSW=0.953; rcor=1; rNcor=1; rlogoDP=8; rNsEucl=1; rNSW=1; rank_mean=2.400; match_rank=1 a 0 0 0 25 5 7 3 9 1 93 1 66 8 0 0 0 c 0 0 0 28 6 2 1 88 2 3 90 23 6 0 0 0 g 0 0 0 11 23 90 3 2 88 1 2 6 66 0 0 0 t 0 0 0 36 66 1 93 1 9 3 7 5 20 0 0 0
DREB1G_MA1032.1_JASPAR_shift3 (DREB1G:MA1032.1:JASPAR)	0.747	0.747	4.900	0.898	0.896	10	2	1	10	10	6.600	3	; dyads_test_vs_ctrl_m1 versus DREB1G_MA1032.1_JASPAR (DREB1G:MA1032.1:JASPAR); m=3/22; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 6.6; ---atGCCGACAt--- ; cor=0.747; Ncor=0.747; logoDP=4.900; NsEucl=0.898; NSW=0.896; rcor=10; rNcor=2; rlogoDP=1; rNsEucl=10; rNSW=10; rank_mean=6.600; match_rank=3 a 0 0 0 314 119 180 0 0 0 884 0 845 131 0 0 0 c 0 0 0 229 226 0 999 999 0 0 999 22 219 0 0 0 g 0 0 0 229 119 820 0 0 999 115 0 22 221 0 0 0 t 0 0 0 229 535 0 0 0 0 0 0 111 430 0 0 0
DREB1A_MA0971.1_JASPAR_rc_shift3 (DREB1A:MA0971.1:JASPAR_rc)	0.737	0.737	4.529	0.901	0.903	12	4	7	6	7	7.200	4	; dyads_test_vs_ctrl_m1 versus DREB1A_MA0971.1_JASPAR_rc (DREB1A:MA0971.1:JASPAR_rc); m=4/22; ncol2=10; w=10; offset=0; strand=R; shift=3; score= 7.2; ---yyrCCGACat--- ; cor=0.737; Ncor=0.737; logoDP=4.529; NsEucl=0.901; NSW=0.903; rcor=12; rNcor=4; rlogoDP=7; rNsEucl=6; rNSW=7; rank_mean=7.200; match_rank=4 a 0 0 0 152 140 461 3 6 1 973 1 565 166 0 0 0 c 0 0 0 322 279 19 948 994 4 3 997 137 126 0 0 0 g 0 0 0 205 240 504 0 0 991 14 0 159 118 0 0 0 t 0 0 0 322 341 16 48 0 5 10 2 139 590 0 0 0
LOC_Os02g45450_M0042_1.02_CISBP_shift3 (LOC_Os02g45450:M0042_1.02:CISBP)	0.746	0.746	4.893	0.898	0.896	11	3	2	11	11	7.600	6	; dyads_test_vs_ctrl_m1 versus LOC_Os02g45450_M0042_1.02_CISBP (LOC_Os02g45450:M0042_1.02:CISBP); m=6/22; ncol2=10; w=10; offset=0; strand=D; shift=3; score= 7.6; ---atGCCGACAt--- ; cor=0.746; Ncor=0.746; logoDP=4.893; NsEucl=0.898; NSW=0.896; rcor=11; rNcor=3; rlogoDP=2; rNsEucl=11; rNSW=11; rank_mean=7.600; match_rank=6 a 0 0 0 31 12 18 0 0 0 88 0 85 13 0 0 0 c 0 0 0 23 23 0 100 100 0 0 100 2 22 0 0 0 g 0 0 0 23 12 82 0 0 100 12 0 2 22 0 0 0 t 0 0 0 23 53 0 0 0 0 0 0 11 43 0 0 0