One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.145021_KMIt8O/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_2019-07-04.145021_KMIt8O/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift9 ; 111 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_shift9 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=9; ncol=23; ---------trACACGTGTya-- ; Alignment reference a 0 0 0 0 0 0 0 0 0 85 89 278 12 319 20 20 10 17 19 81 121 0 0 c 0 0 0 0 0 0 0 0 0 66 76 31 308 4 297 5 9 5 14 96 70 0 0 g 0 0 0 0 0 0 0 0 0 70 96 14 5 9 5 297 4 308 31 76 66 0 0 t 0 0 0 0 0 0 0 0 0 121 81 19 17 10 20 20 319 12 278 89 85 0 0

BES1_MA0549.1_JASPAR_shift10 (BES1:MA0549.1:JASPAR) 0.893 0.818 6.810 0.936 0.955 24 2 27 20 20 18.600 10
; dyads_test_vs_ctrl_m1 versus BES1_MA0549.1_JASPAR (BES1:MA0549.1:JASPAR); m=10/110; ncol2=11; w=11; offset=1; strand=D; shift=10; score= 18.6; ----------crCACGTGksv-- ; cor=0.893; Ncor=0.818; logoDP=6.810; NsEucl=0.936; NSW=0.955; rcor=24; rNcor=2; rlogoDP=27; rNsEucl=20; rNSW=20; rank_mean=18.600; match_rank=10 a 0 0 0 0 0 0 0 0 0 0 23 41 0 89 0 0 0 3 16 17 36 0 0 c 0 0 0 0 0 0 0 0 0 0 45 8 99 0 99 0 0 0 5 33 29 0 0 g 0 0 0 0 0 0 0 0 0 0 10 50 0 4 0 99 0 96 36 46 33 0 0 t 0 0 0 0 0 0 0 0 0 0 21 0 0 6 0 0 99 0 42 3 1 0 0

ABF1_M0257_1.02_CISBP_shift9 (ABF1:M0257_1.02:CISBP) 0.917 0.841 3.594 0.946 0.967 11 1 74 10 10 21.200 11
; dyads_test_vs_ctrl_m1 versus ABF1_M0257_1.02_CISBP (ABF1:M0257_1.02:CISBP); m=11/110; ncol2=11; w=11; offset=0; strand=D; shift=9; score= 21.2; ---------gdACACGTGkb--- ; cor=0.917; Ncor=0.841; logoDP=3.594; NsEucl=0.946; NSW=0.967; rcor=11; rNcor=1; rlogoDP=74; rNsEucl=10; rNSW=10; rank_mean=21.200; match_rank=11 a 0 0 0 0 0 0 0 0 0 21 26 68 16 73 0 18 0 12 16 18 0 0 0 c 0 0 0 0 0 0 0 0 0 21 16 18 75 8 91 0 10 4 19 28 0 0 0 g 0 0 0 0 0 0 0 0 0 37 33 7 0 10 0 82 0 71 40 28 0 0 0 t 0 0 0 0 0 0 0 0 0 21 25 7 9 9 9 0 90 13 25 26 0 0 0

LOC_Os02g49560_M0327_1.02_CISBP_shift9 (LOC_Os02g49560:M0327_1.02:CISBP) 0.881 0.807 6.303 0.935 0.954 32 4 38 22 21 23.400 13
; dyads_test_vs_ctrl_m1 versus LOC_Os02g49560_M0327_1.02_CISBP (LOC_Os02g49560:M0327_1.02:CISBP); m=13/110; ncol2=11; w=11; offset=0; strand=D; shift=9; score= 23.4; ---------tkcCACGTGwy--- ; cor=0.881; Ncor=0.807; logoDP=6.303; NsEucl=0.935; NSW=0.954; rcor=32; rNcor=4; rlogoDP=38; rNsEucl=22; rNSW=21; rank_mean=23.400; match_rank=13 a 0 0 0 0 0 0 0 0 0 22 18 20 0 100 0 0 0 2 27 21 0 0 0 c 0 0 0 0 0 0 0 0 0 22 18 64 93 0 100 0 0 22 7 29 0 0 0 g 0 0 0 0 0 0 0 0 0 23 39 4 7 0 0 100 0 73 19 21 0 0 0 t 0 0 0 0 0 0 0 0 0 33 25 12 0 0 0 0 100 3 47 29 0 0 0

AT4G18890_MA1333.1_JASPAR_rc_shift9 (AT4G18890:MA1333.1:JASPAR_rc) 0.884 0.811 0.339 0.930 0.946 28 3 101 28 31 38.200 26
; dyads_test_vs_ctrl_m1 versus AT4G18890_MA1333.1_JASPAR_rc (AT4G18890:MA1333.1:JASPAR_rc); m=26/110; ncol2=11; w=11; offset=0; strand=R; shift=9; score= 38.2; ---------ycACACGTGyr--- ; cor=0.884; Ncor=0.811; logoDP=0.339; NsEucl=0.930; NSW=0.946; rcor=28; rNcor=3; rlogoDP=101; rNsEucl=28; rNSW=31; rank_mean=38.200; match_rank=26 a 0 0 0 0 0 0 0 0 0 81 52 405 0 589 0 0 0 1 0 225 0 0 0 c 0 0 0 0 0 0 0 0 0 179 338 60 590 0 589 0 0 0 383 43 0 0 0 g 0 0 0 0 0 0 0 0 0 91 140 74 0 0 0 590 0 589 28 319 0 0 0 t 0 0 0 0 0 0 0 0 0 239 60 51 0 1 1 0 590 0 179 3 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_shift9 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=9; ncol=23; ---------trACACGTGTya-- ; Alignment reference a 0 0 0 0 0 0 0 0 0 85 89 278 12 319 20 20 10 17 19 81 121 0 0 c 0 0 0 0 0 0 0 0 0 66 76 31 308 4 297 5 9 5 14 96 70 0 0 g 0 0 0 0 0 0 0 0 0 70 96 14 5 9 5 297 4 308 31 76 66 0 0 t 0 0 0 0 0 0 0 0 0 121 81 19 17 10 20 20 319 12 278 89 85 0 0
BES1_MA0549.1_JASPAR_shift10 (BES1:MA0549.1:JASPAR)	0.893	0.818	6.810	0.936	0.955	24	2	27	20	20	18.600	10	; dyads_test_vs_ctrl_m1 versus BES1_MA0549.1_JASPAR (BES1:MA0549.1:JASPAR); m=10/110; ncol2=11; w=11; offset=1; strand=D; shift=10; score= 18.6; ----------crCACGTGksv-- ; cor=0.893; Ncor=0.818; logoDP=6.810; NsEucl=0.936; NSW=0.955; rcor=24; rNcor=2; rlogoDP=27; rNsEucl=20; rNSW=20; rank_mean=18.600; match_rank=10 a 0 0 0 0 0 0 0 0 0 0 23 41 0 89 0 0 0 3 16 17 36 0 0 c 0 0 0 0 0 0 0 0 0 0 45 8 99 0 99 0 0 0 5 33 29 0 0 g 0 0 0 0 0 0 0 0 0 0 10 50 0 4 0 99 0 96 36 46 33 0 0 t 0 0 0 0 0 0 0 0 0 0 21 0 0 6 0 0 99 0 42 3 1 0 0
ABF1_M0257_1.02_CISBP_shift9 (ABF1:M0257_1.02:CISBP)	0.917	0.841	3.594	0.946	0.967	11	1	74	10	10	21.200	11	; dyads_test_vs_ctrl_m1 versus ABF1_M0257_1.02_CISBP (ABF1:M0257_1.02:CISBP); m=11/110; ncol2=11; w=11; offset=0; strand=D; shift=9; score= 21.2; ---------gdACACGTGkb--- ; cor=0.917; Ncor=0.841; logoDP=3.594; NsEucl=0.946; NSW=0.967; rcor=11; rNcor=1; rlogoDP=74; rNsEucl=10; rNSW=10; rank_mean=21.200; match_rank=11 a 0 0 0 0 0 0 0 0 0 21 26 68 16 73 0 18 0 12 16 18 0 0 0 c 0 0 0 0 0 0 0 0 0 21 16 18 75 8 91 0 10 4 19 28 0 0 0 g 0 0 0 0 0 0 0 0 0 37 33 7 0 10 0 82 0 71 40 28 0 0 0 t 0 0 0 0 0 0 0 0 0 21 25 7 9 9 9 0 90 13 25 26 0 0 0
LOC_Os02g49560_M0327_1.02_CISBP_shift9 (LOC_Os02g49560:M0327_1.02:CISBP)	0.881	0.807	6.303	0.935	0.954	32	4	38	22	21	23.400	13	; dyads_test_vs_ctrl_m1 versus LOC_Os02g49560_M0327_1.02_CISBP (LOC_Os02g49560:M0327_1.02:CISBP); m=13/110; ncol2=11; w=11; offset=0; strand=D; shift=9; score= 23.4; ---------tkcCACGTGwy--- ; cor=0.881; Ncor=0.807; logoDP=6.303; NsEucl=0.935; NSW=0.954; rcor=32; rNcor=4; rlogoDP=38; rNsEucl=22; rNSW=21; rank_mean=23.400; match_rank=13 a 0 0 0 0 0 0 0 0 0 22 18 20 0 100 0 0 0 2 27 21 0 0 0 c 0 0 0 0 0 0 0 0 0 22 18 64 93 0 100 0 0 22 7 29 0 0 0 g 0 0 0 0 0 0 0 0 0 23 39 4 7 0 0 100 0 73 19 21 0 0 0 t 0 0 0 0 0 0 0 0 0 33 25 12 0 0 0 0 100 3 47 29 0 0 0
AT4G18890_MA1333.1_JASPAR_rc_shift9 (AT4G18890:MA1333.1:JASPAR_rc)	0.884	0.811	0.339	0.930	0.946	28	3	101	28	31	38.200	26	; dyads_test_vs_ctrl_m1 versus AT4G18890_MA1333.1_JASPAR_rc (AT4G18890:MA1333.1:JASPAR_rc); m=26/110; ncol2=11; w=11; offset=0; strand=R; shift=9; score= 38.2; ---------ycACACGTGyr--- ; cor=0.884; Ncor=0.811; logoDP=0.339; NsEucl=0.930; NSW=0.946; rcor=28; rNcor=3; rlogoDP=101; rNsEucl=28; rNSW=31; rank_mean=38.200; match_rank=26 a 0 0 0 0 0 0 0 0 0 81 52 405 0 589 0 0 0 1 0 225 0 0 0 c 0 0 0 0 0 0 0 0 0 179 338 60 590 0 589 0 0 0 383 43 0 0 0 g 0 0 0 0 0 0 0 0 0 91 140 74 0 0 0 590 0 589 28 319 0 0 0 t 0 0 0 0 0 0 0 0 0 239 60 51 0 1 1 0 590 0 179 3 0 0 0