One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.154940_mQ2ZoH/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_2019-07-04.154940_mQ2ZoH/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift5 ; 9 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_shift5 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=5; ncol=20; -----yhaACGCGGTtk--- ; Alignment reference a 0 0 0 0 0 57 65 125 215 7 12 11 8 6 29 60 56 0 0 0 c 0 0 0 0 0 65 69 24 9 226 3 218 11 29 14 40 44 0 0 0 g 0 0 0 0 0 43 38 45 7 6 225 4 221 181 15 56 63 0 0 0 t 0 0 0 0 0 78 71 49 12 4 3 10 3 27 185 87 80 0 0 0

CMTA3_MA0970.1_JASPAR_rc_shift5 (CMTA3:MA0970.1:JASPAR_rc) 0.953 0.714 0.158 0.956 0.983 1 3 8 1 1 2.800 1
; dyads_test_vs_ctrl_m1 versus CMTA3_MA0970.1_JASPAR_rc (CMTA3:MA0970.1:JASPAR_rc); m=1/8; ncol2=9; w=9; offset=0; strand=R; shift=5; score= 2.8; -----vyrACrCGg------ ; cor=0.953; Ncor=0.714; logoDP=0.158; NsEucl=0.956; NSW=0.983; rcor=1; rNcor=3; rlogoDP=8; rNsEucl=1; rNSW=1; rank_mean=2.800; match_rank=1 a 0 0 0 0 0 251 213 285 998 0 267 6 8 43 0 0 0 0 0 0 c 0 0 0 0 0 251 250 211 0 963 1 962 5 184 0 0 0 0 0 0 g 0 0 0 0 0 258 247 274 1 0 664 0 974 540 0 0 0 0 0 0 t 0 0 0 0 0 241 290 231 1 37 68 32 14 233 0 0 0 0 0 0

CAMTA3_M0581_1.02_CISBP_rc_shift5 (CAMTA3:M0581_1.02:CISBP_rc) 0.951 0.713 0.158 0.955 0.982 2 4 7 2 2 3.400 2
; dyads_test_vs_ctrl_m1 versus CAMTA3_M0581_1.02_CISBP_rc (CAMTA3:M0581_1.02:CISBP_rc); m=2/8; ncol2=9; w=9; offset=0; strand=R; shift=5; score= 3.4; -----vbrACrCGg------ ; cor=0.951; Ncor=0.713; logoDP=0.158; NsEucl=0.955; NSW=0.982; rcor=2; rNcor=4; rlogoDP=7; rNsEucl=2; rNSW=2; rank_mean=3.400; match_rank=2 a 0 0 0 0 0 25 21 28 100 0 27 1 1 4 0 0 0 0 0 0 c 0 0 0 0 0 25 25 21 0 96 0 96 0 18 0 0 0 0 0 0 g 0 0 0 0 0 26 25 27 0 0 66 0 97 54 0 0 0 0 0 0 t 0 0 0 0 0 24 29 24 0 4 7 3 2 24 0 0 0 0 0 0

CAMTA1_MA1197.1_JASPAR_rc_shift5 (CAMTA1:MA1197.1:JASPAR_rc) 0.879 0.879 5.248 0.939 0.956 5 1 2 5 5 3.600 4
; dyads_test_vs_ctrl_m1 versus CAMTA1_MA1197.1_JASPAR_rc (CAMTA1:MA1197.1:JASPAR_rc); m=4/8; ncol2=12; w=12; offset=0; strand=R; shift=5; score= 3.6; -----yhmACGCGytTt--- ; cor=0.879; Ncor=0.879; logoDP=5.248; NsEucl=0.939; NSW=0.956; rcor=5; rNcor=1; rlogoDP=2; rNsEucl=5; rNSW=5; rank_mean=3.600; match_rank=4 a 0 0 0 0 0 133 174 151 595 0 20 0 0 1 55 77 124 0 0 0 c 0 0 0 0 0 170 156 326 3 598 0 598 0 285 132 45 117 0 0 0 g 0 0 0 0 0 58 33 58 0 0 578 0 598 140 6 46 56 0 0 0 t 0 0 0 0 0 237 235 63 0 0 0 0 0 172 405 430 301 0 0 0

FHY3_MA0557.1_JASPAR_shift5 (FHY3:MA0557.1:JASPAR) 0.752 0.752 5.257 0.914 0.911 8 2 1 8 8 5.400 6
; dyads_test_vs_ctrl_m1 versus FHY3_MA0557.1_JASPAR (FHY3:MA0557.1:JASPAR); m=6/8; ncol2=12; w=12; offset=0; strand=D; shift=5; score= 5.4; -----ywCACGCGCThw--- ; cor=0.752; Ncor=0.752; logoDP=5.257; NsEucl=0.914; NSW=0.911; rcor=8; rNcor=2; rlogoDP=1; rNsEucl=8; rNSW=8; rank_mean=5.400; match_rank=6 a 0 0 0 0 0 46 75 9 226 2 3 0 4 18 16 63 82 0 0 0 c 0 0 0 0 0 81 58 210 3 230 16 220 0 208 40 68 44 0 0 0 g 0 0 0 0 0 40 25 9 2 1 213 0 228 6 17 40 50 0 0 0 t 0 0 0 0 0 68 77 7 4 2 3 15 3 3 162 64 59 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_shift5 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=5; ncol=20; -----yhaACGCGGTtk--- ; Alignment reference a 0 0 0 0 0 57 65 125 215 7 12 11 8 6 29 60 56 0 0 0 c 0 0 0 0 0 65 69 24 9 226 3 218 11 29 14 40 44 0 0 0 g 0 0 0 0 0 43 38 45 7 6 225 4 221 181 15 56 63 0 0 0 t 0 0 0 0 0 78 71 49 12 4 3 10 3 27 185 87 80 0 0 0
CMTA3_MA0970.1_JASPAR_rc_shift5 (CMTA3:MA0970.1:JASPAR_rc)	0.953	0.714	0.158	0.956	0.983	1	3	8	1	1	2.800	1	; dyads_test_vs_ctrl_m1 versus CMTA3_MA0970.1_JASPAR_rc (CMTA3:MA0970.1:JASPAR_rc); m=1/8; ncol2=9; w=9; offset=0; strand=R; shift=5; score= 2.8; -----vyrACrCGg------ ; cor=0.953; Ncor=0.714; logoDP=0.158; NsEucl=0.956; NSW=0.983; rcor=1; rNcor=3; rlogoDP=8; rNsEucl=1; rNSW=1; rank_mean=2.800; match_rank=1 a 0 0 0 0 0 251 213 285 998 0 267 6 8 43 0 0 0 0 0 0 c 0 0 0 0 0 251 250 211 0 963 1 962 5 184 0 0 0 0 0 0 g 0 0 0 0 0 258 247 274 1 0 664 0 974 540 0 0 0 0 0 0 t 0 0 0 0 0 241 290 231 1 37 68 32 14 233 0 0 0 0 0 0
CAMTA3_M0581_1.02_CISBP_rc_shift5 (CAMTA3:M0581_1.02:CISBP_rc)	0.951	0.713	0.158	0.955	0.982	2	4	7	2	2	3.400	2	; dyads_test_vs_ctrl_m1 versus CAMTA3_M0581_1.02_CISBP_rc (CAMTA3:M0581_1.02:CISBP_rc); m=2/8; ncol2=9; w=9; offset=0; strand=R; shift=5; score= 3.4; -----vbrACrCGg------ ; cor=0.951; Ncor=0.713; logoDP=0.158; NsEucl=0.955; NSW=0.982; rcor=2; rNcor=4; rlogoDP=7; rNsEucl=2; rNSW=2; rank_mean=3.400; match_rank=2 a 0 0 0 0 0 25 21 28 100 0 27 1 1 4 0 0 0 0 0 0 c 0 0 0 0 0 25 25 21 0 96 0 96 0 18 0 0 0 0 0 0 g 0 0 0 0 0 26 25 27 0 0 66 0 97 54 0 0 0 0 0 0 t 0 0 0 0 0 24 29 24 0 4 7 3 2 24 0 0 0 0 0 0
CAMTA1_MA1197.1_JASPAR_rc_shift5 (CAMTA1:MA1197.1:JASPAR_rc)	0.879	0.879	5.248	0.939	0.956	5	1	2	5	5	3.600	4	; dyads_test_vs_ctrl_m1 versus CAMTA1_MA1197.1_JASPAR_rc (CAMTA1:MA1197.1:JASPAR_rc); m=4/8; ncol2=12; w=12; offset=0; strand=R; shift=5; score= 3.6; -----yhmACGCGytTt--- ; cor=0.879; Ncor=0.879; logoDP=5.248; NsEucl=0.939; NSW=0.956; rcor=5; rNcor=1; rlogoDP=2; rNsEucl=5; rNSW=5; rank_mean=3.600; match_rank=4 a 0 0 0 0 0 133 174 151 595 0 20 0 0 1 55 77 124 0 0 0 c 0 0 0 0 0 170 156 326 3 598 0 598 0 285 132 45 117 0 0 0 g 0 0 0 0 0 58 33 58 0 0 578 0 598 140 6 46 56 0 0 0 t 0 0 0 0 0 237 235 63 0 0 0 0 0 172 405 430 301 0 0 0
FHY3_MA0557.1_JASPAR_shift5 (FHY3:MA0557.1:JASPAR)	0.752	0.752	5.257	0.914	0.911	8	2	1	8	8	5.400	6	; dyads_test_vs_ctrl_m1 versus FHY3_MA0557.1_JASPAR (FHY3:MA0557.1:JASPAR); m=6/8; ncol2=12; w=12; offset=0; strand=D; shift=5; score= 5.4; -----ywCACGCGCThw--- ; cor=0.752; Ncor=0.752; logoDP=5.257; NsEucl=0.914; NSW=0.911; rcor=8; rNcor=2; rlogoDP=1; rNsEucl=8; rNSW=8; rank_mean=5.400; match_rank=6 a 0 0 0 0 0 46 75 9 226 2 3 0 4 18 16 63 82 0 0 0 c 0 0 0 0 0 81 58 210 3 230 16 220 0 208 40 68 44 0 0 0 g 0 0 0 0 0 40 25 9 2 1 213 0 228 6 17 40 50 0 0 0 t 0 0 0 0 0 68 77 7 4 2 3 15 3 3 162 64 59 0 0 0