One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.154917_TUQtHH/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_2019-07-04.154917_TUQtHH/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m2_shift7 ; 15 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=17; shift=7; ncol=24; -------whccAcACGCGgTttay ; Alignment reference a 0 0 0 0 0 0 0 73 56 53 27 154 26 201 11 23 11 15 24 18 30 48 61 49 c 0 0 0 0 0 0 0 43 62 78 121 16 146 5 198 6 187 7 34 16 27 47 55 58 g 0 0 0 0 0 0 0 39 40 48 28 25 31 12 6 186 7 190 128 17 24 35 54 53 t 0 0 0 0 0 0 0 68 65 44 47 28 20 5 8 8 18 11 37 172 142 93 53 63

CAMTA1_MA1197.1_JASPAR_rc_shift10 (CAMTA1:MA1197.1:JASPAR_rc) 0.906 0.640 4.118 0.946 0.965 3 2 3 2 4 2.800 1
; oligos_5-8nt_m2 versus CAMTA1_MA1197.1_JASPAR_rc (CAMTA1:MA1197.1:JASPAR_rc); m=1/14; ncol2=12; w=12; offset=3; strand=R; shift=10; score= 2.8; ----------yhmACGCGytTt-- ; cor=0.906; Ncor=0.640; logoDP=4.118; NsEucl=0.946; NSW=0.965; rcor=3; rNcor=2; rlogoDP=3; rNsEucl=2; rNSW=4; rank_mean=2.800; 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 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 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 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 0

FHY3_MA0557.1_JASPAR_shift10 (FHY3:MA0557.1:JASPAR) 0.827 0.584 4.533 0.927 0.937 7 3 2 8 7 5.400 4
; oligos_5-8nt_m2 versus FHY3_MA0557.1_JASPAR (FHY3:MA0557.1:JASPAR); m=4/14; ncol2=12; w=12; offset=3; strand=D; shift=10; score= 5.4; ----------ywCACGCGCThw-- ; cor=0.827; Ncor=0.584; logoDP=4.533; NsEucl=0.927; NSW=0.937; rcor=7; rNcor=3; rlogoDP=2; rNsEucl=8; rNSW=7; rank_mean=5.400; match_rank=4 a 0 0 0 0 0 0 0 0 0 0 46 75 9 226 2 3 0 4 18 16 63 82 0 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 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 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 0

FAR1_MA1382.1_JASPAR_shift8 (FAR1:MA1382.1:JASPAR) 0.763 0.673 5.465 0.928 0.921 9 1 1 7 10 5.600 5
; oligos_5-8nt_m2 versus FAR1_MA1382.1_JASPAR (FAR1:MA1382.1:JASPAR); m=5/14; ncol2=15; w=15; offset=1; strand=D; shift=8; score= 5.6; --------ayyyCACGCGCytyy- ; cor=0.763; Ncor=0.673; logoDP=5.465; NsEucl=0.928; NSW=0.921; rcor=9; rNcor=1; rlogoDP=1; rNsEucl=7; rNSW=10; rank_mean=5.600; 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 0 c 0 0 0 0 0 0 0 0 117 191 236 193 550 0 591 0 587 0 586 321 62 212 219 0 g 0 0 0 0 0 0 0 0 98 97 58 13 17 0 0 591 0 590 0 50 147 82 66 0 t 0 0 0 0 0 0 0 0 142 181 224 259 16 0 0 0 4 1 5 193 270 152 171 0

CBT_OsCBT_Athamap_rc_shift5 (CBT:OsCBT:Athamap_rc) 0.723 0.495 0.537 0.917 0.910 14 4 7 10 13 9.600 10
; oligos_5-8nt_m2 versus CBT_OsCBT_Athamap_rc (CBT:OsCBT:Athamap_rc); m=10/14; ncol2=15; w=13; offset=-2; strand=R; shift=5; score= 9.6; -----CGmAmmmmACrCGka---- ; cor=0.723; Ncor=0.495; logoDP=0.537; NsEucl=0.917; NSW=0.910; rcor=14; rNcor=4; rlogoDP=7; rNsEucl=10; rNSW=13; rank_mean=9.600; match_rank=10 a 0 0 0 0 0 2 3 29 75 32 36 40 45 75 0 26 0 0 6 45 0 0 0 0 c 0 0 0 0 0 76 0 35 0 32 24 24 21 3 79 0 79 0 19 10 0 0 0 0 g 0 0 0 0 0 0 76 4 4 8 9 8 4 1 0 53 0 79 26 9 0 0 0 0 t 0 0 0 0 0 1 0 11 0 7 10 7 9 0 0 0 0 0 28 14 0 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=17; shift=7; ncol=24; -------whccAcACGCGgTttay ; Alignment reference a 0 0 0 0 0 0 0 73 56 53 27 154 26 201 11 23 11 15 24 18 30 48 61 49 c 0 0 0 0 0 0 0 43 62 78 121 16 146 5 198 6 187 7 34 16 27 47 55 58 g 0 0 0 0 0 0 0 39 40 48 28 25 31 12 6 186 7 190 128 17 24 35 54 53 t 0 0 0 0 0 0 0 68 65 44 47 28 20 5 8 8 18 11 37 172 142 93 53 63
CAMTA1_MA1197.1_JASPAR_rc_shift10 (CAMTA1:MA1197.1:JASPAR_rc)	0.906	0.640	4.118	0.946	0.965	3	2	3	2	4	2.800	1	; oligos_5-8nt_m2 versus CAMTA1_MA1197.1_JASPAR_rc (CAMTA1:MA1197.1:JASPAR_rc); m=1/14; ncol2=12; w=12; offset=3; strand=R; shift=10; score= 2.8; ----------yhmACGCGytTt-- ; cor=0.906; Ncor=0.640; logoDP=4.118; NsEucl=0.946; NSW=0.965; rcor=3; rNcor=2; rlogoDP=3; rNsEucl=2; rNSW=4; rank_mean=2.800; 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 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 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 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 0
FHY3_MA0557.1_JASPAR_shift10 (FHY3:MA0557.1:JASPAR)	0.827	0.584	4.533	0.927	0.937	7	3	2	8	7	5.400	4	; oligos_5-8nt_m2 versus FHY3_MA0557.1_JASPAR (FHY3:MA0557.1:JASPAR); m=4/14; ncol2=12; w=12; offset=3; strand=D; shift=10; score= 5.4; ----------ywCACGCGCThw-- ; cor=0.827; Ncor=0.584; logoDP=4.533; NsEucl=0.927; NSW=0.937; rcor=7; rNcor=3; rlogoDP=2; rNsEucl=8; rNSW=7; rank_mean=5.400; match_rank=4 a 0 0 0 0 0 0 0 0 0 0 46 75 9 226 2 3 0 4 18 16 63 82 0 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 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 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 0
FAR1_MA1382.1_JASPAR_shift8 (FAR1:MA1382.1:JASPAR)	0.763	0.673	5.465	0.928	0.921	9	1	1	7	10	5.600	5	; oligos_5-8nt_m2 versus FAR1_MA1382.1_JASPAR (FAR1:MA1382.1:JASPAR); m=5/14; ncol2=15; w=15; offset=1; strand=D; shift=8; score= 5.6; --------ayyyCACGCGCytyy- ; cor=0.763; Ncor=0.673; logoDP=5.465; NsEucl=0.928; NSW=0.921; rcor=9; rNcor=1; rlogoDP=1; rNsEucl=7; rNSW=10; rank_mean=5.600; 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 0 c 0 0 0 0 0 0 0 0 117 191 236 193 550 0 591 0 587 0 586 321 62 212 219 0 g 0 0 0 0 0 0 0 0 98 97 58 13 17 0 0 591 0 590 0 50 147 82 66 0 t 0 0 0 0 0 0 0 0 142 181 224 259 16 0 0 0 4 1 5 193 270 152 171 0
CBT_OsCBT_Athamap_rc_shift5 (CBT:OsCBT:Athamap_rc)	0.723	0.495	0.537	0.917	0.910	14	4	7	10	13	9.600	10	; oligos_5-8nt_m2 versus CBT_OsCBT_Athamap_rc (CBT:OsCBT:Athamap_rc); m=10/14; ncol2=15; w=13; offset=-2; strand=R; shift=5; score= 9.6; -----CGmAmmmmACrCGka---- ; cor=0.723; Ncor=0.495; logoDP=0.537; NsEucl=0.917; NSW=0.910; rcor=14; rNcor=4; rlogoDP=7; rNsEucl=10; rNSW=13; rank_mean=9.600; match_rank=10 a 0 0 0 0 0 2 3 29 75 32 36 40 45 75 0 26 0 0 6 45 0 0 0 0 c 0 0 0 0 0 76 0 35 0 32 24 24 21 3 79 0 79 0 19 10 0 0 0 0 g 0 0 0 0 0 0 76 4 4 8 9 8 4 1 0 53 0 79 26 9 0 0 0 0 t 0 0 0 0 0 1 0 11 0 7 10 7 9 0 0 0 0 0 28 14 0 0 0 0