One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/02/compare-matrices_2019-07-02.162658_W9OgcQ/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/2019/07/02/compare-matrices_2019-07-02.162658_W9OgcQ/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift9 ; 125 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_m1_shift9 (oligos_5-8nt_m1)
; oligos_5-8nt_m1; m=0 (reference); ncol1=14; shift=9; ncol=23; ---------wwgaCACGTGtcww ; Alignment reference a 0 0 0 0 0 0 0 0 0 228 205 177 480 32 709 22 33 20 55 121 150 264 234 c 0 0 0 0 0 0 0 0 0 151 161 131 109 644 10 707 7 35 31 67 308 146 159 g 0 0 0 0 0 0 0 0 0 158 145 319 66 38 35 7 712 8 656 111 137 164 152 t 0 0 0 0 0 0 0 0 0 236 262 146 118 59 19 37 21 710 31 474 178 199 228

ABF2_MA0941.1_JASPAR_shift8 (ABF2:MA0941.1:JASPAR) 0.966 0.773 5.026 0.970 0.989 5 3 64 1 1 14.800 1
; oligos_5-8nt_m1 versus ABF2_MA0941.1_JASPAR (ABF2:MA0941.1:JASPAR); m=1/124; ncol2=13; w=12; offset=-1; strand=D; shift=8; score= 14.8; --------cayrACACGTgkt-- ; cor=0.966; Ncor=0.773; logoDP=5.026; NsEucl=0.970; NSW=0.989; rcor=5; rNcor=3; rlogoDP=64; rNsEucl=1; rNSW=1; rank_mean=14.800; match_rank=1 a 0 0 0 0 0 0 0 0 231 308 191 274 699 0 999 0 19 19 218 213 229 0 0 c 0 0 0 0 0 0 0 0 308 231 268 120 177 840 0 917 19 19 59 130 229 0 0 g 0 0 0 0 0 0 0 0 231 231 191 403 103 0 0 0 942 19 664 287 229 0 0 t 0 0 0 0 0 0 0 0 231 231 350 202 21 159 0 82 19 942 59 371 312 0 0

ATAREB1_M0256_1.02_CISBP_shift8 (ATAREB1:M0256_1.02:CISBP) 0.966 0.773 5.002 0.970 0.989 6 4 65 2 2 15.800 2
; oligos_5-8nt_m1 versus ATAREB1_M0256_1.02_CISBP (ATAREB1:M0256_1.02:CISBP); m=2/124; ncol2=13; w=12; offset=-1; strand=D; shift=8; score= 15.8; --------cayrACACGTgkt-- ; cor=0.966; Ncor=0.773; logoDP=5.002; NsEucl=0.970; NSW=0.989; rcor=6; rNcor=4; rlogoDP=65; rNsEucl=2; rNSW=2; rank_mean=15.800; match_rank=2 a 0 0 0 0 0 0 0 0 23 31 19 27 70 0 100 0 2 2 22 21 23 0 0 c 0 0 0 0 0 0 0 0 31 23 27 12 18 84 0 92 2 2 6 13 23 0 0 g 0 0 0 0 0 0 0 0 23 23 19 41 10 0 0 0 94 2 66 29 23 0 0 t 0 0 0 0 0 0 0 0 23 23 35 20 2 16 0 8 2 94 6 37 31 0 0

BZR1_MA0550.1_JASPAR_rc_shift9 (BZR1:MA0550.1:JASPAR_rc) 0.921 0.921 6.412 0.957 0.974 24 1 35 10 15 17.000 5
; oligos_5-8nt_m1 versus BZR1_MA0550.1_JASPAR_rc (BZR1:MA0550.1:JASPAR_rc); m=5/124; ncol2=14; w=14; offset=0; strand=R; shift=9; score= 17; ---------kkbhCACGTGkmkk ; cor=0.921; Ncor=0.921; logoDP=6.412; NsEucl=0.957; NSW=0.974; rcor=24; rNcor=1; rlogoDP=35; rNsEucl=10; rNSW=15; rank_mean=17.000; match_rank=5 a 0 0 0 0 0 0 0 0 0 33 28 16 72 0 153 0 0 4 0 12 51 24 0 c 0 0 0 0 0 0 0 0 0 0 22 43 39 142 0 153 0 0 0 26 52 27 30 g 0 0 0 0 0 0 0 0 0 39 61 53 0 5 0 0 147 2 153 66 20 47 60 t 0 0 0 0 0 0 0 0 0 81 42 41 42 6 0 0 6 147 0 49 30 55 63

HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR) 0.903 0.790 6.419 0.945 0.957 49 2 32 25 47 31.000 14
; oligos_5-8nt_m1 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=14/124; ncol2=16; w=14; offset=-1; strand=D; shift=8; score= 31; --------wwtGmCACGTGkCaw ; cor=0.903; Ncor=0.790; logoDP=6.419; NsEucl=0.945; NSW=0.957; rcor=49; rNcor=2; rlogoDP=32; rNsEucl=25; rNSW=47; rank_mean=31.000; match_rank=14 a 0 0 0 0 0 0 0 0 103 108 52 9 150 0 310 3 1 0 2 4 24 183 94 c 0 0 0 0 0 0 0 0 60 56 55 8 165 317 1 311 5 9 1 1 279 30 62 g 0 0 0 0 0 0 0 0 68 62 30 279 1 1 9 5 311 1 317 165 8 55 56 t 0 0 0 0 0 0 0 0 89 94 183 24 4 2 0 1 3 310 0 150 9 52 108

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m1_shift9 (oligos_5-8nt_m1)													; oligos_5-8nt_m1; m=0 (reference); ncol1=14; shift=9; ncol=23; ---------wwgaCACGTGtcww ; Alignment reference a 0 0 0 0 0 0 0 0 0 228 205 177 480 32 709 22 33 20 55 121 150 264 234 c 0 0 0 0 0 0 0 0 0 151 161 131 109 644 10 707 7 35 31 67 308 146 159 g 0 0 0 0 0 0 0 0 0 158 145 319 66 38 35 7 712 8 656 111 137 164 152 t 0 0 0 0 0 0 0 0 0 236 262 146 118 59 19 37 21 710 31 474 178 199 228
ABF2_MA0941.1_JASPAR_shift8 (ABF2:MA0941.1:JASPAR)	0.966	0.773	5.026	0.970	0.989	5	3	64	1	1	14.800	1	; oligos_5-8nt_m1 versus ABF2_MA0941.1_JASPAR (ABF2:MA0941.1:JASPAR); m=1/124; ncol2=13; w=12; offset=-1; strand=D; shift=8; score= 14.8; --------cayrACACGTgkt-- ; cor=0.966; Ncor=0.773; logoDP=5.026; NsEucl=0.970; NSW=0.989; rcor=5; rNcor=3; rlogoDP=64; rNsEucl=1; rNSW=1; rank_mean=14.800; match_rank=1 a 0 0 0 0 0 0 0 0 231 308 191 274 699 0 999 0 19 19 218 213 229 0 0 c 0 0 0 0 0 0 0 0 308 231 268 120 177 840 0 917 19 19 59 130 229 0 0 g 0 0 0 0 0 0 0 0 231 231 191 403 103 0 0 0 942 19 664 287 229 0 0 t 0 0 0 0 0 0 0 0 231 231 350 202 21 159 0 82 19 942 59 371 312 0 0
ATAREB1_M0256_1.02_CISBP_shift8 (ATAREB1:M0256_1.02:CISBP)	0.966	0.773	5.002	0.970	0.989	6	4	65	2	2	15.800	2	; oligos_5-8nt_m1 versus ATAREB1_M0256_1.02_CISBP (ATAREB1:M0256_1.02:CISBP); m=2/124; ncol2=13; w=12; offset=-1; strand=D; shift=8; score= 15.8; --------cayrACACGTgkt-- ; cor=0.966; Ncor=0.773; logoDP=5.002; NsEucl=0.970; NSW=0.989; rcor=6; rNcor=4; rlogoDP=65; rNsEucl=2; rNSW=2; rank_mean=15.800; match_rank=2 a 0 0 0 0 0 0 0 0 23 31 19 27 70 0 100 0 2 2 22 21 23 0 0 c 0 0 0 0 0 0 0 0 31 23 27 12 18 84 0 92 2 2 6 13 23 0 0 g 0 0 0 0 0 0 0 0 23 23 19 41 10 0 0 0 94 2 66 29 23 0 0 t 0 0 0 0 0 0 0 0 23 23 35 20 2 16 0 8 2 94 6 37 31 0 0
BZR1_MA0550.1_JASPAR_rc_shift9 (BZR1:MA0550.1:JASPAR_rc)	0.921	0.921	6.412	0.957	0.974	24	1	35	10	15	17.000	5	; oligos_5-8nt_m1 versus BZR1_MA0550.1_JASPAR_rc (BZR1:MA0550.1:JASPAR_rc); m=5/124; ncol2=14; w=14; offset=0; strand=R; shift=9; score= 17; ---------kkbhCACGTGkmkk ; cor=0.921; Ncor=0.921; logoDP=6.412; NsEucl=0.957; NSW=0.974; rcor=24; rNcor=1; rlogoDP=35; rNsEucl=10; rNSW=15; rank_mean=17.000; match_rank=5 a 0 0 0 0 0 0 0 0 0 33 28 16 72 0 153 0 0 4 0 12 51 24 0 c 0 0 0 0 0 0 0 0 0 0 22 43 39 142 0 153 0 0 0 26 52 27 30 g 0 0 0 0 0 0 0 0 0 39 61 53 0 5 0 0 147 2 153 66 20 47 60 t 0 0 0 0 0 0 0 0 0 81 42 41 42 6 0 0 6 147 0 49 30 55 63
HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR)	0.903	0.790	6.419	0.945	0.957	49	2	32	25	47	31.000	14	; oligos_5-8nt_m1 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=14/124; ncol2=16; w=14; offset=-1; strand=D; shift=8; score= 31; --------wwtGmCACGTGkCaw ; cor=0.903; Ncor=0.790; logoDP=6.419; NsEucl=0.945; NSW=0.957; rcor=49; rNcor=2; rlogoDP=32; rNsEucl=25; rNSW=47; rank_mean=31.000; match_rank=14 a 0 0 0 0 0 0 0 0 103 108 52 9 150 0 310 3 1 0 2 4 24 183 94 c 0 0 0 0 0 0 0 0 60 56 55 8 165 317 1 311 5 9 1 1 279 30 62 g 0 0 0 0 0 0 0 0 68 62 30 279 1 1 9 5 311 1 317 165 8 55 56 t 0 0 0 0 0 0 0 0 89 94 183 24 4 2 0 1 3 310 0 150 9 52 108