One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.160049_kyPEVL/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_2019-07-04.160049_kyPEVL/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m5_shift9 ; 46 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_m5_shift9 (oligos_5-8nt_m5)
; oligos_5-8nt_m5; m=0 (reference); ncol1=13; shift=9; ncol=23; ---------mmmcACGCGctyy- ; Alignment reference a 0 0 0 0 0 0 0 0 0 16 17 37 13 55 2 2 4 3 3 8 11 14 0 c 0 0 0 0 0 0 0 0 0 24 21 18 42 0 59 1 56 1 40 6 17 17 0 g 0 0 0 0 0 0 0 0 0 10 13 5 4 7 1 58 0 57 8 9 13 11 0 t 0 0 0 0 0 0 0 0 0 13 12 3 4 1 1 2 3 2 12 40 22 21 0

FHY3_MA0557.1_JASPAR_shift10 (FHY3:MA0557.1:JASPAR) 0.952 0.879 5.574 0.960 0.981 1 1 7 1 1 2.200 1
; oligos_5-8nt_m5 versus FHY3_MA0557.1_JASPAR (FHY3:MA0557.1:JASPAR); m=1/45; ncol2=12; w=12; offset=1; strand=D; shift=10; score= 2.2; ----------ywCACGCGCThw- ; cor=0.952; Ncor=0.879; logoDP=5.574; NsEucl=0.960; NSW=0.981; rcor=1; rNcor=1; rlogoDP=7; rNsEucl=1; rNSW=1; rank_mean=2.200; match_rank=1 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) 0.897 0.777 6.894 0.943 0.957 5 3 1 5 5 3.800 2
; oligos_5-8nt_m5 versus FAR1_MA1382.1_JASPAR (FAR1:MA1382.1:JASPAR); m=2/45; ncol2=15; w=13; offset=-1; strand=D; shift=8; score= 3.8; --------ayyyCACGCGCytyy ; cor=0.897; Ncor=0.777; logoDP=6.894; NsEucl=0.943; NSW=0.957; rcor=5; rNcor=3; rlogoDP=1; rNsEucl=5; rNSW=5; rank_mean=3.800; match_rank=2 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

CAMTA1_MA1197.1_JASPAR_rc_shift10 (CAMTA1:MA1197.1:JASPAR_rc) 0.926 0.855 5.302 0.952 0.972 4 2 10 2 4 4.400 3
; oligos_5-8nt_m5 versus CAMTA1_MA1197.1_JASPAR_rc (CAMTA1:MA1197.1:JASPAR_rc); m=3/45; ncol2=12; w=12; offset=1; strand=R; shift=10; score= 4.4; ----------yhmACGCGytTt- ; cor=0.926; Ncor=0.855; logoDP=5.302; NsEucl=0.952; NSW=0.972; rcor=4; rNcor=2; rlogoDP=10; rNsEucl=2; rNSW=4; rank_mean=4.400; match_rank=3 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

MYB88.DAP_M0513_AthalianaCistrome_shift8 (MYB88.DAP:M0513:AthalianaCistrome) 0.792 0.687 4.741 0.930 0.936 14 4 15 9 12 10.800 5
; oligos_5-8nt_m5 versus MYB88.DAP_M0513_AthalianaCistrome (MYB88.DAP:M0513:AthalianaCistrome); m=5/45; ncol2=15; w=13; offset=-1; strand=D; shift=8; score= 10.8; --------hmymcACGCkCCwcy ; cor=0.792; Ncor=0.687; logoDP=4.741; NsEucl=0.930; NSW=0.936; rcor=14; rNcor=4; rlogoDP=15; rNsEucl=9; rNSW=12; rank_mean=10.800; match_rank=5 a 0 0 0 0 0 0 0 0 177 161 122 214 82 472 21 0 0 0 0 5 160 100 108 c 0 0 0 0 0 0 0 0 151 179 217 174 304 111 545 0 594 0 588 482 61 296 276 g 0 0 0 0 0 0 0 0 101 113 87 59 95 11 28 594 0 301 0 5 122 70 61 t 0 0 0 0 0 0 0 0 165 141 168 147 113 0 0 0 0 293 6 102 251 128 149

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m5_shift9 (oligos_5-8nt_m5)													; oligos_5-8nt_m5; m=0 (reference); ncol1=13; shift=9; ncol=23; ---------mmmcACGCGctyy- ; Alignment reference a 0 0 0 0 0 0 0 0 0 16 17 37 13 55 2 2 4 3 3 8 11 14 0 c 0 0 0 0 0 0 0 0 0 24 21 18 42 0 59 1 56 1 40 6 17 17 0 g 0 0 0 0 0 0 0 0 0 10 13 5 4 7 1 58 0 57 8 9 13 11 0 t 0 0 0 0 0 0 0 0 0 13 12 3 4 1 1 2 3 2 12 40 22 21 0
FHY3_MA0557.1_JASPAR_shift10 (FHY3:MA0557.1:JASPAR)	0.952	0.879	5.574	0.960	0.981	1	1	7	1	1	2.200	1	; oligos_5-8nt_m5 versus FHY3_MA0557.1_JASPAR (FHY3:MA0557.1:JASPAR); m=1/45; ncol2=12; w=12; offset=1; strand=D; shift=10; score= 2.2; ----------ywCACGCGCThw- ; cor=0.952; Ncor=0.879; logoDP=5.574; NsEucl=0.960; NSW=0.981; rcor=1; rNcor=1; rlogoDP=7; rNsEucl=1; rNSW=1; rank_mean=2.200; match_rank=1 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)	0.897	0.777	6.894	0.943	0.957	5	3	1	5	5	3.800	2	; oligos_5-8nt_m5 versus FAR1_MA1382.1_JASPAR (FAR1:MA1382.1:JASPAR); m=2/45; ncol2=15; w=13; offset=-1; strand=D; shift=8; score= 3.8; --------ayyyCACGCGCytyy ; cor=0.897; Ncor=0.777; logoDP=6.894; NsEucl=0.943; NSW=0.957; rcor=5; rNcor=3; rlogoDP=1; rNsEucl=5; rNSW=5; rank_mean=3.800; match_rank=2 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
CAMTA1_MA1197.1_JASPAR_rc_shift10 (CAMTA1:MA1197.1:JASPAR_rc)	0.926	0.855	5.302	0.952	0.972	4	2	10	2	4	4.400	3	; oligos_5-8nt_m5 versus CAMTA1_MA1197.1_JASPAR_rc (CAMTA1:MA1197.1:JASPAR_rc); m=3/45; ncol2=12; w=12; offset=1; strand=R; shift=10; score= 4.4; ----------yhmACGCGytTt- ; cor=0.926; Ncor=0.855; logoDP=5.302; NsEucl=0.952; NSW=0.972; rcor=4; rNcor=2; rlogoDP=10; rNsEucl=2; rNSW=4; rank_mean=4.400; match_rank=3 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
MYB88.DAP_M0513_AthalianaCistrome_shift8 (MYB88.DAP:M0513:AthalianaCistrome)	0.792	0.687	4.741	0.930	0.936	14	4	15	9	12	10.800	5	; oligos_5-8nt_m5 versus MYB88.DAP_M0513_AthalianaCistrome (MYB88.DAP:M0513:AthalianaCistrome); m=5/45; ncol2=15; w=13; offset=-1; strand=D; shift=8; score= 10.8; --------hmymcACGCkCCwcy ; cor=0.792; Ncor=0.687; logoDP=4.741; NsEucl=0.930; NSW=0.936; rcor=14; rNcor=4; rlogoDP=15; rNsEucl=9; rNSW=12; rank_mean=10.800; match_rank=5 a 0 0 0 0 0 0 0 0 177 161 122 214 82 472 21 0 0 0 0 5 160 100 108 c 0 0 0 0 0 0 0 0 151 179 217 174 304 111 545 0 594 0 588 482 61 296 276 g 0 0 0 0 0 0 0 0 101 113 87 59 95 11 28 594 0 301 0 5 122 70 61 t 0 0 0 0 0 0 0 0 165 141 168 147 113 0 0 0 0 293 6 102 251 128 149