One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/07/compare-matrices_2019-07-07.150749_f2UiMH/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_2019-07-07.150749_f2UiMH/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift0 ; 7 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_shift0 (oligos_5-8nt_m1)
; oligos_5-8nt_m1; m=0 (reference); ncol1=11; shift=0; ncol=13; wwCTCGCAwrw-- ; Alignment reference a 11 11 0 4 0 0 0 33 9 9 9 0 0 c 7 8 33 0 34 0 25 0 5 1 7 0 0 g 6 4 1 4 0 33 3 1 3 17 6 0 0 t 10 11 0 26 0 1 6 0 17 7 12 0 0

TOE1_TOE1_ArabidopsisPBM_shift0 (TOE1:TOE1:ArabidopsisPBM) 0.701 0.637 5.885 0.885 0.869 6 1 2 2 4 3.000 2
; oligos_5-8nt_m1 versus TOE1_TOE1_ArabidopsisPBM (TOE1:TOE1:ArabidopsisPBM); m=2/6; ncol2=10; w=10; offset=0; strand=D; shift=0; score= 3; WCCTCGTACy--- ; cor=0.701; Ncor=0.637; logoDP=5.885; NsEucl=0.885; NSW=0.869; rcor=6; rNcor=1; rlogoDP=2; rNsEucl=2; rNSW=4; rank_mean=3.000; match_rank=2 a 69 1 13 0 5 1 1 96 5 23 0 0 0 c 2 88 84 1 93 1 0 2 80 31 0 0 0 g 2 0 1 1 2 97 19 0 5 21 0 0 0 t 27 11 2 98 0 1 80 2 10 25 0 0 0

TOE1_TOE1_2_ArabidopsisPBM_rc_shift3 (TOE1:TOE1_2:ArabidopsisPBM_rc) 0.737 0.454 0.733 0.883 0.891 3 3 5 3 2 3.200 3
; oligos_5-8nt_m1 versus TOE1_TOE1_2_ArabidopsisPBM_rc (TOE1:TOE1_2:ArabidopsisPBM_rc); m=3/6; ncol2=10; w=8; offset=3; strand=R; shift=3; score= 3.2; ---TCsYAgGTTy ; cor=0.737; Ncor=0.454; logoDP=0.733; NsEucl=0.883; NSW=0.891; rcor=3; rNcor=3; rlogoDP=5; rNsEucl=3; rNSW=2; rank_mean=3.200; match_rank=3 a 0 0 0 6 3 4 4 92 2 3 19 18 21 c 0 0 0 1 93 25 26 1 21 2 1 4 32 g 0 0 0 3 1 63 2 3 64 92 1 3 5 t 0 0 0 90 3 8 68 4 13 3 79 75 42

FUS3_MA0565.1_JASPAR_shift4 (FUS3:MA0565.1:JASPAR) 0.772 0.416 4.233 0.865 0.872 2 4 3 4 3 3.200 4
; oligos_5-8nt_m1 versus FUS3_MA0565.1_JASPAR (FUS3:MA0565.1:JASPAR); m=4/6; ncol2=9; w=7; offset=4; strand=D; shift=4; score= 3.2; ----yGCATGCrs ; cor=0.772; Ncor=0.416; logoDP=4.233; NsEucl=0.865; NSW=0.872; rcor=2; rNcor=4; rlogoDP=3; rNsEucl=4; rNSW=3; rank_mean=3.200; match_rank=4 a 0 0 0 0 8 1 1 99 1 0 1 29 15 c 0 0 0 0 61 2 99 0 0 0 97 3 44 g 0 0 0 0 4 97 0 0 1 99 2 59 25 t 0 0 0 0 28 1 0 1 99 1 1 9 16

At3g54990_MA0553.1_JASPAR_shift1 (At3g54990:MA0553.1:JASPAR) 0.710 0.516 6.601 0.860 0.842 5 2 1 5 6 3.800 5
; oligos_5-8nt_m1 versus At3g54990_MA0553.1_JASPAR (At3g54990:MA0553.1:JASPAR); m=5/6; ncol2=8; w=8; offset=1; strand=D; shift=1; score= 3.8; -YCTCGTAC---- ; cor=0.710; Ncor=0.516; logoDP=6.601; NsEucl=0.860; NSW=0.842; rcor=5; rNcor=2; rlogoDP=1; rNsEucl=5; rNSW=6; rank_mean=3.800; match_rank=5 a 0 0 0 0 0 0 0 135 0 0 0 0 0 c 0 105 119 0 147 0 0 12 147 0 0 0 0 g 0 0 28 0 0 147 25 0 0 0 0 0 0 t 0 42 0 147 0 0 122 0 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m1_shift0 (oligos_5-8nt_m1)													; oligos_5-8nt_m1; m=0 (reference); ncol1=11; shift=0; ncol=13; wwCTCGCAwrw-- ; Alignment reference a 11 11 0 4 0 0 0 33 9 9 9 0 0 c 7 8 33 0 34 0 25 0 5 1 7 0 0 g 6 4 1 4 0 33 3 1 3 17 6 0 0 t 10 11 0 26 0 1 6 0 17 7 12 0 0
TOE1_TOE1_ArabidopsisPBM_shift0 (TOE1:TOE1:ArabidopsisPBM)	0.701	0.637	5.885	0.885	0.869	6	1	2	2	4	3.000	2	; oligos_5-8nt_m1 versus TOE1_TOE1_ArabidopsisPBM (TOE1:TOE1:ArabidopsisPBM); m=2/6; ncol2=10; w=10; offset=0; strand=D; shift=0; score= 3; WCCTCGTACy--- ; cor=0.701; Ncor=0.637; logoDP=5.885; NsEucl=0.885; NSW=0.869; rcor=6; rNcor=1; rlogoDP=2; rNsEucl=2; rNSW=4; rank_mean=3.000; match_rank=2 a 69 1 13 0 5 1 1 96 5 23 0 0 0 c 2 88 84 1 93 1 0 2 80 31 0 0 0 g 2 0 1 1 2 97 19 0 5 21 0 0 0 t 27 11 2 98 0 1 80 2 10 25 0 0 0
TOE1_TOE1_2_ArabidopsisPBM_rc_shift3 (TOE1:TOE1_2:ArabidopsisPBM_rc)	0.737	0.454	0.733	0.883	0.891	3	3	5	3	2	3.200	3	; oligos_5-8nt_m1 versus TOE1_TOE1_2_ArabidopsisPBM_rc (TOE1:TOE1_2:ArabidopsisPBM_rc); m=3/6; ncol2=10; w=8; offset=3; strand=R; shift=3; score= 3.2; ---TCsYAgGTTy ; cor=0.737; Ncor=0.454; logoDP=0.733; NsEucl=0.883; NSW=0.891; rcor=3; rNcor=3; rlogoDP=5; rNsEucl=3; rNSW=2; rank_mean=3.200; match_rank=3 a 0 0 0 6 3 4 4 92 2 3 19 18 21 c 0 0 0 1 93 25 26 1 21 2 1 4 32 g 0 0 0 3 1 63 2 3 64 92 1 3 5 t 0 0 0 90 3 8 68 4 13 3 79 75 42
FUS3_MA0565.1_JASPAR_shift4 (FUS3:MA0565.1:JASPAR)	0.772	0.416	4.233	0.865	0.872	2	4	3	4	3	3.200	4	; oligos_5-8nt_m1 versus FUS3_MA0565.1_JASPAR (FUS3:MA0565.1:JASPAR); m=4/6; ncol2=9; w=7; offset=4; strand=D; shift=4; score= 3.2; ----yGCATGCrs ; cor=0.772; Ncor=0.416; logoDP=4.233; NsEucl=0.865; NSW=0.872; rcor=2; rNcor=4; rlogoDP=3; rNsEucl=4; rNSW=3; rank_mean=3.200; match_rank=4 a 0 0 0 0 8 1 1 99 1 0 1 29 15 c 0 0 0 0 61 2 99 0 0 0 97 3 44 g 0 0 0 0 4 97 0 0 1 99 2 59 25 t 0 0 0 0 28 1 0 1 99 1 1 9 16
At3g54990_MA0553.1_JASPAR_shift1 (At3g54990:MA0553.1:JASPAR)	0.710	0.516	6.601	0.860	0.842	5	2	1	5	6	3.800	5	; oligos_5-8nt_m1 versus At3g54990_MA0553.1_JASPAR (At3g54990:MA0553.1:JASPAR); m=5/6; ncol2=8; w=8; offset=1; strand=D; shift=1; score= 3.8; -YCTCGTAC---- ; cor=0.710; Ncor=0.516; logoDP=6.601; NsEucl=0.860; NSW=0.842; rcor=5; rNcor=2; rlogoDP=1; rNsEucl=5; rNSW=6; rank_mean=3.800; match_rank=5 a 0 0 0 0 0 0 0 135 0 0 0 0 0 c 0 105 119 0 147 0 0 12 147 0 0 0 0 g 0 0 28 0 0 147 25 0 0 0 0 0 0 t 0 42 0 147 0 0 122 0 0 0 0 0 0