One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.155309_pTUEkS/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_2019-07-04.155309_pTUEkS/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m2_shift7 ; 26 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

oligos_5-8nt_m2_shift7 (oligos_5-8nt_m2)
; oligos_5-8nt_m2; m=0 (reference); ncol1=16; shift=7; ncol=23; -------wmwcACACGCGgTkwt ; Alignment reference a 0 0 0 0 0 0 0 51 48 40 20 109 15 139 7 12 6 11 20 13 20 42 33 c 0 0 0 0 0 0 0 30 42 27 94 12 109 3 142 4 125 7 15 17 20 33 37 g 0 0 0 0 0 0 0 27 32 35 19 16 16 6 2 128 3 124 93 15 75 33 36 t 0 0 0 0 0 0 0 46 32 52 21 17 14 6 3 10 20 12 26 109 39 46 48

CAMTA1_MA1197.1_JASPAR_rc_shift10 (CAMTA1:MA1197.1:JASPAR_rc) 0.832 0.624 4.047 0.929 0.939 5 2 7 3 5 4.400 1
; oligos_5-8nt_m2 versus CAMTA1_MA1197.1_JASPAR_rc (CAMTA1:MA1197.1:JASPAR_rc); m=1/25; ncol2=12; w=12; offset=3; strand=R; shift=10; score= 4.4; ----------yhmACGCGytTt- ; cor=0.832; Ncor=0.624; logoDP=4.047; NsEucl=0.929; NSW=0.939; rcor=5; rNcor=2; rlogoDP=7; rNsEucl=3; rNSW=5; rank_mean=4.400; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 133 174 151 595 0 20 0 0 1 55 77 124 0 c 0 0 0 0 0 0 0 0 0 0 170 156 326 3 598 0 598 0 285 132 45 117 0 g 0 0 0 0 0 0 0 0 0 0 58 33 58 0 0 578 0 598 140 6 46 56 0 t 0 0 0 0 0 0 0 0 0 0 237 235 63 0 0 0 0 0 172 405 430 301 0

FHY3_MA0557.1_JASPAR_shift10 (FHY3:MA0557.1:JASPAR) 0.816 0.612 4.503 0.926 0.933 6 3 4 5 7 5.000 2
; oligos_5-8nt_m2 versus FHY3_MA0557.1_JASPAR (FHY3:MA0557.1:JASPAR); m=2/25; ncol2=12; w=12; offset=3; strand=D; shift=10; score= 5; ----------ywCACGCGCThw- ; cor=0.816; Ncor=0.612; logoDP=4.503; NsEucl=0.926; NSW=0.933; rcor=6; rNcor=3; rlogoDP=4; rNsEucl=5; rNSW=7; rank_mean=5.000; match_rank=2 a 0 0 0 0 0 0 0 0 0 0 46 75 9 226 2 3 0 4 18 16 63 82 0 c 0 0 0 0 0 0 0 0 0 0 81 58 210 3 230 16 220 0 208 40 68 44 0 g 0 0 0 0 0 0 0 0 0 0 40 25 9 2 1 213 0 228 6 17 40 50 0 t 0 0 0 0 0 0 0 0 0 0 68 77 7 4 2 3 15 3 3 162 64 59 0

FAR1_MA1382.1_JASPAR_shift8 (FAR1:MA1382.1:JASPAR) 0.747 0.700 5.439 0.925 0.917 10 1 1 6 12 6.000 5
; oligos_5-8nt_m2 versus FAR1_MA1382.1_JASPAR (FAR1:MA1382.1:JASPAR); m=5/25; ncol2=15; w=15; offset=1; strand=D; shift=8; score= 6; --------ayyyCACGCGCytyy ; cor=0.747; Ncor=0.700; logoDP=5.439; NsEucl=0.925; NSW=0.917; rcor=10; rNcor=1; rlogoDP=1; rNsEucl=6; rNSW=12; rank_mean=6.000; match_rank=5 a 0 0 0 0 0 0 0 0 234 122 73 126 8 591 0 0 0 0 0 27 112 145 135 c 0 0 0 0 0 0 0 0 117 191 236 193 550 0 591 0 587 0 586 321 62 212 219 g 0 0 0 0 0 0 0 0 98 97 58 13 17 0 0 591 0 590 0 50 147 82 66 t 0 0 0 0 0 0 0 0 142 181 224 259 16 0 0 0 4 1 5 193 270 152 171

ATAREB1_M0256_1.02_CISBP_shift7 (ATAREB1:M0256_1.02:CISBP) 0.707 0.574 3.522 0.920 0.916 24 5 9 9 13 12.000 10
; oligos_5-8nt_m2 versus ATAREB1_M0256_1.02_CISBP (ATAREB1:M0256_1.02:CISBP); m=10/25; ncol2=13; w=13; offset=0; strand=D; shift=7; score= 12; -------cayrACACGTgkt--- ; cor=0.707; Ncor=0.574; logoDP=3.522; NsEucl=0.920; NSW=0.916; rcor=24; rNcor=5; rlogoDP=9; rNsEucl=9; rNSW=13; rank_mean=12.000; match_rank=10 a 0 0 0 0 0 0 0 23 31 19 27 70 0 100 0 2 2 22 21 23 0 0 0 c 0 0 0 0 0 0 0 31 23 27 12 18 84 0 92 2 2 6 13 23 0 0 0 g 0 0 0 0 0 0 0 23 23 19 41 10 0 0 0 94 2 66 29 23 0 0 0 t 0 0 0 0 0 0 0 23 23 35 20 2 16 0 8 2 94 6 37 31 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m2_shift7 (oligos_5-8nt_m2)													; oligos_5-8nt_m2; m=0 (reference); ncol1=16; shift=7; ncol=23; -------wmwcACACGCGgTkwt ; Alignment reference a 0 0 0 0 0 0 0 51 48 40 20 109 15 139 7 12 6 11 20 13 20 42 33 c 0 0 0 0 0 0 0 30 42 27 94 12 109 3 142 4 125 7 15 17 20 33 37 g 0 0 0 0 0 0 0 27 32 35 19 16 16 6 2 128 3 124 93 15 75 33 36 t 0 0 0 0 0 0 0 46 32 52 21 17 14 6 3 10 20 12 26 109 39 46 48
CAMTA1_MA1197.1_JASPAR_rc_shift10 (CAMTA1:MA1197.1:JASPAR_rc)	0.832	0.624	4.047	0.929	0.939	5	2	7	3	5	4.400	1	; oligos_5-8nt_m2 versus CAMTA1_MA1197.1_JASPAR_rc (CAMTA1:MA1197.1:JASPAR_rc); m=1/25; ncol2=12; w=12; offset=3; strand=R; shift=10; score= 4.4; ----------yhmACGCGytTt- ; cor=0.832; Ncor=0.624; logoDP=4.047; NsEucl=0.929; NSW=0.939; rcor=5; rNcor=2; rlogoDP=7; rNsEucl=3; rNSW=5; rank_mean=4.400; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 133 174 151 595 0 20 0 0 1 55 77 124 0 c 0 0 0 0 0 0 0 0 0 0 170 156 326 3 598 0 598 0 285 132 45 117 0 g 0 0 0 0 0 0 0 0 0 0 58 33 58 0 0 578 0 598 140 6 46 56 0 t 0 0 0 0 0 0 0 0 0 0 237 235 63 0 0 0 0 0 172 405 430 301 0
FHY3_MA0557.1_JASPAR_shift10 (FHY3:MA0557.1:JASPAR)	0.816	0.612	4.503	0.926	0.933	6	3	4	5	7	5.000	2	; oligos_5-8nt_m2 versus FHY3_MA0557.1_JASPAR (FHY3:MA0557.1:JASPAR); m=2/25; ncol2=12; w=12; offset=3; strand=D; shift=10; score= 5; ----------ywCACGCGCThw- ; cor=0.816; Ncor=0.612; logoDP=4.503; NsEucl=0.926; NSW=0.933; rcor=6; rNcor=3; rlogoDP=4; rNsEucl=5; rNSW=7; rank_mean=5.000; match_rank=2 a 0 0 0 0 0 0 0 0 0 0 46 75 9 226 2 3 0 4 18 16 63 82 0 c 0 0 0 0 0 0 0 0 0 0 81 58 210 3 230 16 220 0 208 40 68 44 0 g 0 0 0 0 0 0 0 0 0 0 40 25 9 2 1 213 0 228 6 17 40 50 0 t 0 0 0 0 0 0 0 0 0 0 68 77 7 4 2 3 15 3 3 162 64 59 0
FAR1_MA1382.1_JASPAR_shift8 (FAR1:MA1382.1:JASPAR)	0.747	0.700	5.439	0.925	0.917	10	1	1	6	12	6.000	5	; oligos_5-8nt_m2 versus FAR1_MA1382.1_JASPAR (FAR1:MA1382.1:JASPAR); m=5/25; ncol2=15; w=15; offset=1; strand=D; shift=8; score= 6; --------ayyyCACGCGCytyy ; cor=0.747; Ncor=0.700; logoDP=5.439; NsEucl=0.925; NSW=0.917; rcor=10; rNcor=1; rlogoDP=1; rNsEucl=6; rNSW=12; rank_mean=6.000; match_rank=5 a 0 0 0 0 0 0 0 0 234 122 73 126 8 591 0 0 0 0 0 27 112 145 135 c 0 0 0 0 0 0 0 0 117 191 236 193 550 0 591 0 587 0 586 321 62 212 219 g 0 0 0 0 0 0 0 0 98 97 58 13 17 0 0 591 0 590 0 50 147 82 66 t 0 0 0 0 0 0 0 0 142 181 224 259 16 0 0 0 4 1 5 193 270 152 171
ATAREB1_M0256_1.02_CISBP_shift7 (ATAREB1:M0256_1.02:CISBP)	0.707	0.574	3.522	0.920	0.916	24	5	9	9	13	12.000	10	; oligos_5-8nt_m2 versus ATAREB1_M0256_1.02_CISBP (ATAREB1:M0256_1.02:CISBP); m=10/25; ncol2=13; w=13; offset=0; strand=D; shift=7; score= 12; -------cayrACACGTgkt--- ; cor=0.707; Ncor=0.574; logoDP=3.522; NsEucl=0.920; NSW=0.916; rcor=24; rNcor=5; rlogoDP=9; rNsEucl=9; rNSW=13; rank_mean=12.000; match_rank=10 a 0 0 0 0 0 0 0 23 31 19 27 70 0 100 0 2 2 22 21 23 0 0 0 c 0 0 0 0 0 0 0 31 23 27 12 18 84 0 92 2 2 6 13 23 0 0 0 g 0 0 0 0 0 0 0 23 23 19 41 10 0 0 0 94 2 66 29 23 0 0 0 t 0 0 0 0 0 0 0 23 23 35 20 2 16 0 8 2 94 6 37 31 0 0 0