One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.155354_wocBcq/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_2019-07-04.155354_wocBcq/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m3_shift3 ; 13 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_m3_shift3 (dyads_test_vs_ctrl_m3)
; dyads_test_vs_ctrl_m3; m=0 (reference); ncol1=17; shift=3; ncol=22; ---rvcacACGCGgTttcby-- ; Alignment reference a 0 0 0 28 26 13 61 12 84 4 8 6 6 4 4 13 14 12 16 23 0 0 c 0 0 0 22 25 53 8 54 3 89 0 83 1 12 9 12 11 45 24 24 0 0 g 0 0 0 25 24 13 13 16 6 1 85 2 81 65 5 14 12 23 25 20 0 0 t 0 0 0 21 21 17 14 14 3 2 3 5 8 15 78 57 59 16 31 29 0 0

CAMTA1_MA1197.1_JASPAR_rc_shift5 (CAMTA1:MA1197.1:JASPAR_rc) 0.900 0.636 4.721 0.944 0.963 3 2 3 1 1 2.000 1
; dyads_test_vs_ctrl_m3 versus CAMTA1_MA1197.1_JASPAR_rc (CAMTA1:MA1197.1:JASPAR_rc); m=1/12; ncol2=12; w=12; offset=2; strand=R; shift=5; score= 2; -----yhmACGCGytTt----- ; cor=0.900; Ncor=0.636; logoDP=4.721; NsEucl=0.944; NSW=0.963; rcor=3; rNcor=2; rlogoDP=3; rNsEucl=1; rNSW=1; rank_mean=2.000; match_rank=1 a 0 0 0 0 0 133 174 151 595 0 20 0 0 1 55 77 124 0 0 0 0 0 c 0 0 0 0 0 170 156 326 3 598 0 598 0 285 132 45 117 0 0 0 0 0 g 0 0 0 0 0 58 33 58 0 0 578 0 598 140 6 46 56 0 0 0 0 0 t 0 0 0 0 0 237 235 63 0 0 0 0 0 172 405 430 301 0 0 0 0 0

CMTA2_MA0969.1_JASPAR_rc_shift8 (CMTA2:MA0969.1:JASPAR_rc) 0.902 0.478 0.840 0.935 0.962 2 5 7 3 3 4.000 3
; dyads_test_vs_ctrl_m3 versus CMTA2_MA0969.1_JASPAR_rc (CMTA2:MA0969.1:JASPAR_rc); m=3/12; ncol2=9; w=9; offset=5; strand=R; shift=8; score= 4; --------ACRCGstww----- ; cor=0.902; Ncor=0.478; logoDP=0.840; NsEucl=0.935; NSW=0.962; rcor=2; rNcor=5; rlogoDP=7; rNsEucl=3; rNSW=3; rank_mean=4.000; match_rank=3 a 0 0 0 0 0 0 0 0 928 15 280 1 11 36 243 260 264 0 0 0 0 0 c 0 0 0 0 0 0 0 0 54 970 7 970 8 306 243 176 220 0 0 0 0 0 g 0 0 0 0 0 0 0 0 11 7 682 11 955 438 121 237 203 0 0 0 0 0 t 0 0 0 0 0 0 0 0 7 8 31 18 26 220 393 327 313 0 0 0 0 0

FAR1_MA1382.1_JASPAR_shift3 (FAR1:MA1382.1:JASPAR) 0.733 0.647 5.862 0.923 0.910 8 1 1 7 9 5.200 4
; dyads_test_vs_ctrl_m3 versus FAR1_MA1382.1_JASPAR (FAR1:MA1382.1:JASPAR); m=4/12; ncol2=15; w=15; offset=0; strand=D; shift=3; score= 5.2; ---ayyyCACGCGCytyy---- ; cor=0.733; Ncor=0.647; logoDP=5.862; NsEucl=0.923; NSW=0.910; rcor=8; rNcor=1; rlogoDP=1; rNsEucl=7; rNSW=9; rank_mean=5.200; match_rank=4 a 0 0 0 234 122 73 126 8 591 0 0 0 0 0 27 112 145 135 0 0 0 0 c 0 0 0 117 191 236 193 550 0 591 0 587 0 586 321 62 212 219 0 0 0 0 g 0 0 0 98 97 58 13 17 0 0 591 0 590 0 50 147 82 66 0 0 0 0 t 0 0 0 142 181 224 259 16 0 0 0 4 1 5 193 270 152 171 0 0 0 0

FHY3_MA0557.1_JASPAR_shift5 (FHY3:MA0557.1:JASPAR) 0.797 0.563 4.846 0.921 0.925 7 3 2 8 8 5.600 5
; dyads_test_vs_ctrl_m3 versus FHY3_MA0557.1_JASPAR (FHY3:MA0557.1:JASPAR); m=5/12; ncol2=12; w=12; offset=2; strand=D; shift=5; score= 5.6; -----ywCACGCGCThw----- ; cor=0.797; Ncor=0.563; logoDP=4.846; NsEucl=0.921; NSW=0.925; rcor=7; rNcor=3; rlogoDP=2; rNsEucl=8; rNSW=8; rank_mean=5.600; match_rank=5 a 0 0 0 0 0 46 75 9 226 2 3 0 4 18 16 63 82 0 0 0 0 0 c 0 0 0 0 0 81 58 210 3 230 16 220 0 208 40 68 44 0 0 0 0 0 g 0 0 0 0 0 40 25 9 2 1 213 0 228 6 17 40 50 0 0 0 0 0 t 0 0 0 0 0 68 77 7 4 2 3 15 3 3 162 64 59 0 0 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_m3_shift3 (dyads_test_vs_ctrl_m3)													; dyads_test_vs_ctrl_m3; m=0 (reference); ncol1=17; shift=3; ncol=22; ---rvcacACGCGgTttcby-- ; Alignment reference a 0 0 0 28 26 13 61 12 84 4 8 6 6 4 4 13 14 12 16 23 0 0 c 0 0 0 22 25 53 8 54 3 89 0 83 1 12 9 12 11 45 24 24 0 0 g 0 0 0 25 24 13 13 16 6 1 85 2 81 65 5 14 12 23 25 20 0 0 t 0 0 0 21 21 17 14 14 3 2 3 5 8 15 78 57 59 16 31 29 0 0
CAMTA1_MA1197.1_JASPAR_rc_shift5 (CAMTA1:MA1197.1:JASPAR_rc)	0.900	0.636	4.721	0.944	0.963	3	2	3	1	1	2.000	1	; dyads_test_vs_ctrl_m3 versus CAMTA1_MA1197.1_JASPAR_rc (CAMTA1:MA1197.1:JASPAR_rc); m=1/12; ncol2=12; w=12; offset=2; strand=R; shift=5; score= 2; -----yhmACGCGytTt----- ; cor=0.900; Ncor=0.636; logoDP=4.721; NsEucl=0.944; NSW=0.963; rcor=3; rNcor=2; rlogoDP=3; rNsEucl=1; rNSW=1; rank_mean=2.000; match_rank=1 a 0 0 0 0 0 133 174 151 595 0 20 0 0 1 55 77 124 0 0 0 0 0 c 0 0 0 0 0 170 156 326 3 598 0 598 0 285 132 45 117 0 0 0 0 0 g 0 0 0 0 0 58 33 58 0 0 578 0 598 140 6 46 56 0 0 0 0 0 t 0 0 0 0 0 237 235 63 0 0 0 0 0 172 405 430 301 0 0 0 0 0
CMTA2_MA0969.1_JASPAR_rc_shift8 (CMTA2:MA0969.1:JASPAR_rc)	0.902	0.478	0.840	0.935	0.962	2	5	7	3	3	4.000	3	; dyads_test_vs_ctrl_m3 versus CMTA2_MA0969.1_JASPAR_rc (CMTA2:MA0969.1:JASPAR_rc); m=3/12; ncol2=9; w=9; offset=5; strand=R; shift=8; score= 4; --------ACRCGstww----- ; cor=0.902; Ncor=0.478; logoDP=0.840; NsEucl=0.935; NSW=0.962; rcor=2; rNcor=5; rlogoDP=7; rNsEucl=3; rNSW=3; rank_mean=4.000; match_rank=3 a 0 0 0 0 0 0 0 0 928 15 280 1 11 36 243 260 264 0 0 0 0 0 c 0 0 0 0 0 0 0 0 54 970 7 970 8 306 243 176 220 0 0 0 0 0 g 0 0 0 0 0 0 0 0 11 7 682 11 955 438 121 237 203 0 0 0 0 0 t 0 0 0 0 0 0 0 0 7 8 31 18 26 220 393 327 313 0 0 0 0 0
FAR1_MA1382.1_JASPAR_shift3 (FAR1:MA1382.1:JASPAR)	0.733	0.647	5.862	0.923	0.910	8	1	1	7	9	5.200	4	; dyads_test_vs_ctrl_m3 versus FAR1_MA1382.1_JASPAR (FAR1:MA1382.1:JASPAR); m=4/12; ncol2=15; w=15; offset=0; strand=D; shift=3; score= 5.2; ---ayyyCACGCGCytyy---- ; cor=0.733; Ncor=0.647; logoDP=5.862; NsEucl=0.923; NSW=0.910; rcor=8; rNcor=1; rlogoDP=1; rNsEucl=7; rNSW=9; rank_mean=5.200; match_rank=4 a 0 0 0 234 122 73 126 8 591 0 0 0 0 0 27 112 145 135 0 0 0 0 c 0 0 0 117 191 236 193 550 0 591 0 587 0 586 321 62 212 219 0 0 0 0 g 0 0 0 98 97 58 13 17 0 0 591 0 590 0 50 147 82 66 0 0 0 0 t 0 0 0 142 181 224 259 16 0 0 0 4 1 5 193 270 152 171 0 0 0 0
FHY3_MA0557.1_JASPAR_shift5 (FHY3:MA0557.1:JASPAR)	0.797	0.563	4.846	0.921	0.925	7	3	2	8	8	5.600	5	; dyads_test_vs_ctrl_m3 versus FHY3_MA0557.1_JASPAR (FHY3:MA0557.1:JASPAR); m=5/12; ncol2=12; w=12; offset=2; strand=D; shift=5; score= 5.6; -----ywCACGCGCThw----- ; cor=0.797; Ncor=0.563; logoDP=4.846; NsEucl=0.921; NSW=0.925; rcor=7; rNcor=3; rlogoDP=2; rNsEucl=8; rNSW=8; rank_mean=5.600; match_rank=5 a 0 0 0 0 0 46 75 9 226 2 3 0 4 18 16 63 82 0 0 0 0 0 c 0 0 0 0 0 81 58 210 3 230 16 220 0 208 40 68 44 0 0 0 0 0 g 0 0 0 0 0 40 25 9 2 1 213 0 228 6 17 40 50 0 0 0 0 0 t 0 0 0 0 0 68 77 7 4 2 3 15 3 3 162 64 59 0 0 0 0 0