One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/07/compare-matrices_2019-07-07.150840_jWFozV/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_2019-07-07.150840_jWFozV/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift0 ; 8 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_shift0 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=10; shift=0; ncol=13; wwCTCGCAwr--- ; Alignment reference a 11 11 0 4 0 0 1 32 9 9 0 0 0 c 7 6 32 0 33 0 25 0 5 2 0 0 0 g 6 4 1 4 0 32 1 1 4 15 0 0 0 t 9 12 0 25 0 1 6 0 15 7 0 0 0

6fas_B_6fas_B_3D-footprint_rc_shift5 (6fas_B:6fas_B:3D-footprint_rc) 0.890 0.445 0.148 0.895 0.945 1 2 7 1 1 2.400 1
; dyads_test_vs_ctrl_m1 versus 6fas_B_6fas_B_3D-footprint_rc (6fas_B:6fas_B:3D-footprint_rc); m=1/7; ncol2=5; w=5; offset=5; strand=R; shift=5; score= 2.4; -----GCATG--- ; cor=0.890; Ncor=0.445; logoDP=0.148; NsEucl=0.895; NSW=0.945; rcor=1; rNcor=2; rlogoDP=7; rNsEucl=1; rNSW=1; rank_mean=2.400; match_rank=1 a 0 0 0 0 0 3 5 83 0 6 0 0 0 c 0 0 0 0 0 0 74 3 5 5 0 0 0 g 0 0 0 0 0 93 4 7 3 81 0 0 0 t 0 0 0 0 0 0 13 3 88 4 0 0 0

At3g54990_MA0553.1_JASPAR_shift1 (At3g54990:MA0553.1:JASPAR) 0.701 0.561 6.557 0.858 0.838 7 1 1 5 7 4.200 4
; dyads_test_vs_ctrl_m1 versus At3g54990_MA0553.1_JASPAR (At3g54990:MA0553.1:JASPAR); m=4/7; ncol2=8; w=8; offset=1; strand=D; shift=1; score= 4.2; -YCTCGTAC---- ; cor=0.701; Ncor=0.561; logoDP=6.557; NsEucl=0.858; NSW=0.838; rcor=7; rNcor=1; rlogoDP=1; rNsEucl=5; rNSW=7; rank_mean=4.200; match_rank=4 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

FUS3_MA0565.1_JASPAR_rc_shift3 (FUS3:MA0565.1:JASPAR_rc) 0.758 0.442 0.172 0.869 0.880 4 3 6 4 4 4.200 5
; dyads_test_vs_ctrl_m1 versus FUS3_MA0565.1_JASPAR_rc (FUS3:MA0565.1:JASPAR_rc); m=5/7; ncol2=9; w=7; offset=3; strand=R; shift=3; score= 4.2; ---syGCATGCr- ; cor=0.758; Ncor=0.442; logoDP=0.172; NsEucl=0.869; NSW=0.880; rcor=4; rNcor=3; rlogoDP=6; rNsEucl=4; rNSW=4; rank_mean=4.200; match_rank=5 a 0 0 0 16 9 1 1 99 1 0 1 28 0 c 0 0 0 25 59 2 99 1 0 0 97 4 0 g 0 0 0 44 3 97 0 0 0 99 2 61 0 t 0 0 0 15 29 1 0 1 99 1 1 8 0

5yzy_C_5yzy_C_3D-footprint_shift4 (5yzy_C:5yzy_C:3D-footprint) 0.724 0.435 4.187 0.849 0.862 5 4 2 6 5 4.400 6
; dyads_test_vs_ctrl_m1 versus 5yzy_C_5yzy_C_3D-footprint (5yzy_C:5yzy_C:3D-footprint); m=6/7; ncol2=6; w=6; offset=4; strand=D; shift=4; score= 4.4; ----tGCATg--- ; cor=0.724; Ncor=0.435; logoDP=4.187; NsEucl=0.849; NSW=0.862; rcor=5; rNcor=4; rlogoDP=2; rNsEucl=6; rNSW=5; rank_mean=4.400; match_rank=6 a 0 0 0 0 16 0 0 96 0 16 0 0 0 c 0 0 0 0 13 0 96 0 0 13 0 0 0 g 0 0 0 0 13 96 0 0 0 54 0 0 0 t 0 0 0 0 54 0 0 0 96 13 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_shift0 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=10; shift=0; ncol=13; wwCTCGCAwr--- ; Alignment reference a 11 11 0 4 0 0 1 32 9 9 0 0 0 c 7 6 32 0 33 0 25 0 5 2 0 0 0 g 6 4 1 4 0 32 1 1 4 15 0 0 0 t 9 12 0 25 0 1 6 0 15 7 0 0 0
6fas_B_6fas_B_3D-footprint_rc_shift5 (6fas_B:6fas_B:3D-footprint_rc)	0.890	0.445	0.148	0.895	0.945	1	2	7	1	1	2.400	1	; dyads_test_vs_ctrl_m1 versus 6fas_B_6fas_B_3D-footprint_rc (6fas_B:6fas_B:3D-footprint_rc); m=1/7; ncol2=5; w=5; offset=5; strand=R; shift=5; score= 2.4; -----GCATG--- ; cor=0.890; Ncor=0.445; logoDP=0.148; NsEucl=0.895; NSW=0.945; rcor=1; rNcor=2; rlogoDP=7; rNsEucl=1; rNSW=1; rank_mean=2.400; match_rank=1 a 0 0 0 0 0 3 5 83 0 6 0 0 0 c 0 0 0 0 0 0 74 3 5 5 0 0 0 g 0 0 0 0 0 93 4 7 3 81 0 0 0 t 0 0 0 0 0 0 13 3 88 4 0 0 0
At3g54990_MA0553.1_JASPAR_shift1 (At3g54990:MA0553.1:JASPAR)	0.701	0.561	6.557	0.858	0.838	7	1	1	5	7	4.200	4	; dyads_test_vs_ctrl_m1 versus At3g54990_MA0553.1_JASPAR (At3g54990:MA0553.1:JASPAR); m=4/7; ncol2=8; w=8; offset=1; strand=D; shift=1; score= 4.2; -YCTCGTAC---- ; cor=0.701; Ncor=0.561; logoDP=6.557; NsEucl=0.858; NSW=0.838; rcor=7; rNcor=1; rlogoDP=1; rNsEucl=5; rNSW=7; rank_mean=4.200; match_rank=4 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
FUS3_MA0565.1_JASPAR_rc_shift3 (FUS3:MA0565.1:JASPAR_rc)	0.758	0.442	0.172	0.869	0.880	4	3	6	4	4	4.200	5	; dyads_test_vs_ctrl_m1 versus FUS3_MA0565.1_JASPAR_rc (FUS3:MA0565.1:JASPAR_rc); m=5/7; ncol2=9; w=7; offset=3; strand=R; shift=3; score= 4.2; ---syGCATGCr- ; cor=0.758; Ncor=0.442; logoDP=0.172; NsEucl=0.869; NSW=0.880; rcor=4; rNcor=3; rlogoDP=6; rNsEucl=4; rNSW=4; rank_mean=4.200; match_rank=5 a 0 0 0 16 9 1 1 99 1 0 1 28 0 c 0 0 0 25 59 2 99 1 0 0 97 4 0 g 0 0 0 44 3 97 0 0 0 99 2 61 0 t 0 0 0 15 29 1 0 1 99 1 1 8 0
5yzy_C_5yzy_C_3D-footprint_shift4 (5yzy_C:5yzy_C:3D-footprint)	0.724	0.435	4.187	0.849	0.862	5	4	2	6	5	4.400	6	; dyads_test_vs_ctrl_m1 versus 5yzy_C_5yzy_C_3D-footprint (5yzy_C:5yzy_C:3D-footprint); m=6/7; ncol2=6; w=6; offset=4; strand=D; shift=4; score= 4.4; ----tGCATg--- ; cor=0.724; Ncor=0.435; logoDP=4.187; NsEucl=0.849; NSW=0.862; rcor=5; rNcor=4; rlogoDP=2; rNsEucl=6; rNSW=5; rank_mean=4.400; match_rank=6 a 0 0 0 0 16 0 0 96 0 16 0 0 0 c 0 0 0 0 13 0 96 0 0 13 0 0 0 g 0 0 0 0 13 96 0 0 0 54 0 0 0 t 0 0 0 0 54 0 0 0 96 13 0 0 0