One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/02/compare-matrices_2019-07-02.130717_Ue5iiO/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/2019/07/02/compare-matrices_2019-07-02.130717_Ue5iiO/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m2_shift1 ; 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

dyads_test_vs_ctrl_m2_shift1 (dyads_test_vs_ctrl_m2)
; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=11; shift=1; ncol=13; -wwaGGsCCAww- ; Alignment reference a 0 563 666 1378 136 95 163 68 90 1861 744 694 0 c 0 404 312 144 35 36 1314 1911 1861 57 434 420 0 g 0 412 450 170 1839 1867 520 25 35 53 320 382 0 t 0 684 635 371 53 65 66 59 77 92 565 567 0

TCP3_M1645_1.02_CISBP_shift2 (TCP3:M1645_1.02:CISBP) 0.791 0.719 3.980 0.916 0.929 1 1 19 1 1 4.600 1
; dyads_test_vs_ctrl_m2 versus TCP3_M1645_1.02_CISBP (TCP3:M1645_1.02:CISBP); m=1/27; ncol2=10; w=10; offset=1; strand=D; shift=2; score= 4.6; --kgGGaCCAch- ; cor=0.791; Ncor=0.719; logoDP=3.980; NsEucl=0.916; NSW=0.929; rcor=1; rNcor=1; rlogoDP=19; rNsEucl=1; rNSW=1; rank_mean=4.600; match_rank=1 a 0 0 17 17 3 3 62 2 3 80 8 29 0 c 0 0 24 5 2 12 24 96 97 7 67 29 0 g 0 0 31 58 91 80 3 2 0 11 11 16 0 t 0 0 28 20 4 5 11 0 0 2 14 26 0

LOC_Os02g42380_M1657_1.02_CISBP_shift1 (LOC_Os02g42380:M1657_1.02:CISBP) 0.730 0.664 3.849 0.904 0.908 8 2 20 4 4 7.600 3
; dyads_test_vs_ctrl_m2 versus LOC_Os02g42380_M1657_1.02_CISBP (LOC_Os02g42380:M1657_1.02:CISBP); m=3/27; ncol2=10; w=10; offset=0; strand=D; shift=1; score= 7.6; -kkGGgcCCmm-- ; cor=0.730; Ncor=0.664; logoDP=3.849; NsEucl=0.904; NSW=0.908; rcor=8; rNcor=2; rlogoDP=20; rNsEucl=4; rNSW=4; rank_mean=7.600; match_rank=3 a 0 18 7 0 0.0000 13 11 0.0000 7 45 28 0 0 c 0 13 15 0 0.0000 10 66 1.0000 93 33 41 0 0 g 0 41 33 93 1.0000 66 10 0.0000 0 15 13 0 0 t 0 28 45 7 0.0000 11 13 0.0000 0 7 18 0 0

OJ1581_MA1031.1_JASPAR_shift1 (OJ1581:MA1031.1:JASPAR) 0.729 0.663 3.844 0.904 0.907 9 3 21 5 5 8.600 4
; dyads_test_vs_ctrl_m2 versus OJ1581_MA1031.1_JASPAR (OJ1581:MA1031.1:JASPAR); m=4/27; ncol2=10; w=10; offset=0; strand=D; shift=1; score= 8.6; -kkGGgcCCmm-- ; cor=0.729; Ncor=0.663; logoDP=3.844; NsEucl=0.904; NSW=0.907; rcor=9; rNcor=3; rlogoDP=21; rNsEucl=5; rNSW=5; rank_mean=8.600; match_rank=4 a 0 175 74 0 0 127 112 0 71 445 279 0 0 c 0 131 146 0 0 101 661 1000 929 335 414 0 0 g 0 414 335 929 1000 661 101 0 0 146 131 0 0 t 0 279 445 71 0 112 127 0 0 74 175 0 0

TCP23_TCP23_ArabidopsisPBM_shift2 (TCP23:TCP23:ArabidopsisPBM) 0.721 0.655 5.349 0.880 0.855 14 4 9 16 21 12.800 9
; dyads_test_vs_ctrl_m2 versus TCP23_TCP23_ArabidopsisPBM (TCP23:TCP23:ArabidopsisPBM); m=9/27; ncol2=10; w=10; offset=1; strand=D; shift=2; score= 12.8; --GGGGCCCACA- ; cor=0.721; Ncor=0.655; logoDP=5.349; NsEucl=0.880; NSW=0.855; rcor=14; rNcor=4; rlogoDP=9; rNsEucl=16; rNSW=21; rank_mean=12.800; match_rank=9 a 0 0 2 0 1 3 1 0 1 96 1 74 0 c 0 0 5 0 1 9 97 98 98 1 96 14 0 g 0 0 77 97 98 84 1 2 0 3 1 2 0 t 0 0 16 3 0 4 1 0 1 0 2 10 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m2_shift1 (dyads_test_vs_ctrl_m2)													; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=11; shift=1; ncol=13; -wwaGGsCCAww- ; Alignment reference a 0 563 666 1378 136 95 163 68 90 1861 744 694 0 c 0 404 312 144 35 36 1314 1911 1861 57 434 420 0 g 0 412 450 170 1839 1867 520 25 35 53 320 382 0 t 0 684 635 371 53 65 66 59 77 92 565 567 0
TCP3_M1645_1.02_CISBP_shift2 (TCP3:M1645_1.02:CISBP)	0.791	0.719	3.980	0.916	0.929	1	1	19	1	1	4.600	1	; dyads_test_vs_ctrl_m2 versus TCP3_M1645_1.02_CISBP (TCP3:M1645_1.02:CISBP); m=1/27; ncol2=10; w=10; offset=1; strand=D; shift=2; score= 4.6; --kgGGaCCAch- ; cor=0.791; Ncor=0.719; logoDP=3.980; NsEucl=0.916; NSW=0.929; rcor=1; rNcor=1; rlogoDP=19; rNsEucl=1; rNSW=1; rank_mean=4.600; match_rank=1 a 0 0 17 17 3 3 62 2 3 80 8 29 0 c 0 0 24 5 2 12 24 96 97 7 67 29 0 g 0 0 31 58 91 80 3 2 0 11 11 16 0 t 0 0 28 20 4 5 11 0 0 2 14 26 0
LOC_Os02g42380_M1657_1.02_CISBP_shift1 (LOC_Os02g42380:M1657_1.02:CISBP)	0.730	0.664	3.849	0.904	0.908	8	2	20	4	4	7.600	3	; dyads_test_vs_ctrl_m2 versus LOC_Os02g42380_M1657_1.02_CISBP (LOC_Os02g42380:M1657_1.02:CISBP); m=3/27; ncol2=10; w=10; offset=0; strand=D; shift=1; score= 7.6; -kkGGgcCCmm-- ; cor=0.730; Ncor=0.664; logoDP=3.849; NsEucl=0.904; NSW=0.908; rcor=8; rNcor=2; rlogoDP=20; rNsEucl=4; rNSW=4; rank_mean=7.600; match_rank=3 a 0 18 7 0 0.0000 13 11 0.0000 7 45 28 0 0 c 0 13 15 0 0.0000 10 66 1.0000 93 33 41 0 0 g 0 41 33 93 1.0000 66 10 0.0000 0 15 13 0 0 t 0 28 45 7 0.0000 11 13 0.0000 0 7 18 0 0
OJ1581_MA1031.1_JASPAR_shift1 (OJ1581:MA1031.1:JASPAR)	0.729	0.663	3.844	0.904	0.907	9	3	21	5	5	8.600	4	; dyads_test_vs_ctrl_m2 versus OJ1581_MA1031.1_JASPAR (OJ1581:MA1031.1:JASPAR); m=4/27; ncol2=10; w=10; offset=0; strand=D; shift=1; score= 8.6; -kkGGgcCCmm-- ; cor=0.729; Ncor=0.663; logoDP=3.844; NsEucl=0.904; NSW=0.907; rcor=9; rNcor=3; rlogoDP=21; rNsEucl=5; rNSW=5; rank_mean=8.600; match_rank=4 a 0 175 74 0 0 127 112 0 71 445 279 0 0 c 0 131 146 0 0 101 661 1000 929 335 414 0 0 g 0 414 335 929 1000 661 101 0 0 146 131 0 0 t 0 279 445 71 0 112 127 0 0 74 175 0 0
TCP23_TCP23_ArabidopsisPBM_shift2 (TCP23:TCP23:ArabidopsisPBM)	0.721	0.655	5.349	0.880	0.855	14	4	9	16	21	12.800	9	; dyads_test_vs_ctrl_m2 versus TCP23_TCP23_ArabidopsisPBM (TCP23:TCP23:ArabidopsisPBM); m=9/27; ncol2=10; w=10; offset=1; strand=D; shift=2; score= 12.8; --GGGGCCCACA- ; cor=0.721; Ncor=0.655; logoDP=5.349; NsEucl=0.880; NSW=0.855; rcor=14; rNcor=4; rlogoDP=9; rNsEucl=16; rNSW=21; rank_mean=12.800; match_rank=9 a 0 0 2 0 1 3 1 0 1 96 1 74 0 c 0 0 5 0 1 9 97 98 98 1 96 14 0 g 0 0 77 97 98 84 1 2 0 3 1 2 0 t 0 0 16 3 0 4 1 0 1 0 2 10 0