One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/02/compare-matrices_2019-07-02.163352_0fwf4a/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_2019-07-02.163352_0fwf4a/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift9 ; 126 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=12; shift=9; ncol=23; ---------wdaCACGTGtmw-- ; Alignment reference a 0 0 0 0 0 0 0 0 0 144 131 308 23 476 9 20 14 36 81 134 188 0 0 c 0 0 0 0 0 0 0 0 0 104 91 82 451 5 488 3 25 8 48 168 83 0 0 g 0 0 0 0 0 0 0 0 0 83 166 50 9 25 3 488 6 454 83 89 104 0 0 t 0 0 0 0 0 0 0 0 0 189 132 80 37 14 20 9 475 22 308 129 145 0 0

BES1_MA0549.1_JASPAR_shift10 (BES1:MA0549.1:JASPAR) 0.920 0.843 7.022 0.945 0.966 38 3 29 29 40 27.800 8
; oligos_5-8nt_m1 versus BES1_MA0549.1_JASPAR (BES1:MA0549.1:JASPAR); m=8/125; ncol2=11; w=11; offset=1; strand=D; shift=10; score= 27.8; ----------crCACGTGksv-- ; cor=0.920; Ncor=0.843; logoDP=7.022; NsEucl=0.945; NSW=0.966; rcor=38; rNcor=3; rlogoDP=29; rNsEucl=29; rNSW=40; rank_mean=27.800; match_rank=8 a 0 0 0 0 0 0 0 0 0 0 23 41 0 89 0 0 0 3 16 17 36 0 0 c 0 0 0 0 0 0 0 0 0 0 45 8 99 0 99 0 0 0 5 33 29 0 0 g 0 0 0 0 0 0 0 0 0 0 10 50 0 4 0 99 0 96 36 46 33 0 0 t 0 0 0 0 0 0 0 0 0 0 21 0 0 6 0 0 99 0 42 3 1 0 0

ABF1_M0257_1.02_CISBP_rc_shift10 (ABF1:M0257_1.02:CISBP_rc) 0.944 0.865 0.320 0.957 0.980 18 1 109 8 13 29.800 11
; oligos_5-8nt_m1 versus ABF1_M0257_1.02_CISBP_rc (ABF1:M0257_1.02:CISBP_rc); m=11/125; ncol2=11; w=11; offset=1; strand=R; shift=10; score= 29.8; ----------vmCACGTGThc-- ; cor=0.944; Ncor=0.865; logoDP=0.320; NsEucl=0.957; NSW=0.980; rcor=18; rNcor=1; rlogoDP=109; rNsEucl=8; rNSW=13; rank_mean=29.800; match_rank=11 a 0 0 0 0 0 0 0 0 0 0 26 25 13 90 0 9 9 9 7 25 21 0 0 c 0 0 0 0 0 0 0 0 0 0 28 40 71 0 82 0 10 0 7 33 37 0 0 g 0 0 0 0 0 0 0 0 0 0 28 19 4 10 0 91 8 75 18 16 21 0 0 t 0 0 0 0 0 0 0 0 0 0 18 16 12 0 18 0 73 16 68 26 21 0 0

LOC_Os02g49560_M0327_1.02_CISBP_rc_shift10 (LOC_Os02g49560:M0327_1.02:CISBP_rc) 0.934 0.856 0.346 0.952 0.975 25 2 107 13 17 32.800 20
; oligos_5-8nt_m1 versus LOC_Os02g49560_M0327_1.02_CISBP_rc (LOC_Os02g49560:M0327_1.02:CISBP_rc); m=20/125; ncol2=11; w=11; offset=1; strand=R; shift=10; score= 32.8; ----------rwCACGTGgma-- ; cor=0.934; Ncor=0.856; logoDP=0.346; NsEucl=0.952; NSW=0.975; rcor=25; rNcor=2; rlogoDP=107; rNsEucl=13; rNSW=17; rank_mean=32.800; match_rank=20 a 0 0 0 0 0 0 0 0 0 0 29 47 3 100 0 0 0 0 12 25 33 0 0 c 0 0 0 0 0 0 0 0 0 0 21 19 73 0 100 0 0 7 4 39 23 0 0 g 0 0 0 0 0 0 0 0 0 0 29 7 22 0 0 100 0 93 64 18 22 0 0 t 0 0 0 0 0 0 0 0 0 0 21 27 2 0 0 0 100 0 20 18 22 0 0

AT4G18890_MA1333.1_JASPAR_shift10 (AT4G18890:MA1333.1:JASPAR) 0.900 0.825 7.605 0.934 0.953 56 4 9 48 54 34.200 22
; oligos_5-8nt_m1 versus AT4G18890_MA1333.1_JASPAR (AT4G18890:MA1333.1:JASPAR); m=22/125; ncol2=11; w=11; offset=1; strand=D; shift=10; score= 34.2; ----------yrCACGTGTgr-- ; cor=0.900; Ncor=0.825; logoDP=7.605; NsEucl=0.934; NSW=0.953; rcor=56; rNcor=4; rlogoDP=9; rNsEucl=48; rNSW=54; rank_mean=34.200; match_rank=22 a 0 0 0 0 0 0 0 0 0 0 3 179 0 590 0 1 1 0 51 60 239 0 0 c 0 0 0 0 0 0 0 0 0 0 319 28 589 0 590 0 0 0 74 140 91 0 0 g 0 0 0 0 0 0 0 0 0 0 43 383 0 0 0 589 0 590 60 338 179 0 0 t 0 0 0 0 0 0 0 0 0 0 225 0 1 0 0 0 589 0 405 52 81 0 0

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=12; shift=9; ncol=23; ---------wdaCACGTGtmw-- ; Alignment reference a 0 0 0 0 0 0 0 0 0 144 131 308 23 476 9 20 14 36 81 134 188 0 0 c 0 0 0 0 0 0 0 0 0 104 91 82 451 5 488 3 25 8 48 168 83 0 0 g 0 0 0 0 0 0 0 0 0 83 166 50 9 25 3 488 6 454 83 89 104 0 0 t 0 0 0 0 0 0 0 0 0 189 132 80 37 14 20 9 475 22 308 129 145 0 0
BES1_MA0549.1_JASPAR_shift10 (BES1:MA0549.1:JASPAR)	0.920	0.843	7.022	0.945	0.966	38	3	29	29	40	27.800	8	; oligos_5-8nt_m1 versus BES1_MA0549.1_JASPAR (BES1:MA0549.1:JASPAR); m=8/125; ncol2=11; w=11; offset=1; strand=D; shift=10; score= 27.8; ----------crCACGTGksv-- ; cor=0.920; Ncor=0.843; logoDP=7.022; NsEucl=0.945; NSW=0.966; rcor=38; rNcor=3; rlogoDP=29; rNsEucl=29; rNSW=40; rank_mean=27.800; match_rank=8 a 0 0 0 0 0 0 0 0 0 0 23 41 0 89 0 0 0 3 16 17 36 0 0 c 0 0 0 0 0 0 0 0 0 0 45 8 99 0 99 0 0 0 5 33 29 0 0 g 0 0 0 0 0 0 0 0 0 0 10 50 0 4 0 99 0 96 36 46 33 0 0 t 0 0 0 0 0 0 0 0 0 0 21 0 0 6 0 0 99 0 42 3 1 0 0
ABF1_M0257_1.02_CISBP_rc_shift10 (ABF1:M0257_1.02:CISBP_rc)	0.944	0.865	0.320	0.957	0.980	18	1	109	8	13	29.800	11	; oligos_5-8nt_m1 versus ABF1_M0257_1.02_CISBP_rc (ABF1:M0257_1.02:CISBP_rc); m=11/125; ncol2=11; w=11; offset=1; strand=R; shift=10; score= 29.8; ----------vmCACGTGThc-- ; cor=0.944; Ncor=0.865; logoDP=0.320; NsEucl=0.957; NSW=0.980; rcor=18; rNcor=1; rlogoDP=109; rNsEucl=8; rNSW=13; rank_mean=29.800; match_rank=11 a 0 0 0 0 0 0 0 0 0 0 26 25 13 90 0 9 9 9 7 25 21 0 0 c 0 0 0 0 0 0 0 0 0 0 28 40 71 0 82 0 10 0 7 33 37 0 0 g 0 0 0 0 0 0 0 0 0 0 28 19 4 10 0 91 8 75 18 16 21 0 0 t 0 0 0 0 0 0 0 0 0 0 18 16 12 0 18 0 73 16 68 26 21 0 0
LOC_Os02g49560_M0327_1.02_CISBP_rc_shift10 (LOC_Os02g49560:M0327_1.02:CISBP_rc)	0.934	0.856	0.346	0.952	0.975	25	2	107	13	17	32.800	20	; oligos_5-8nt_m1 versus LOC_Os02g49560_M0327_1.02_CISBP_rc (LOC_Os02g49560:M0327_1.02:CISBP_rc); m=20/125; ncol2=11; w=11; offset=1; strand=R; shift=10; score= 32.8; ----------rwCACGTGgma-- ; cor=0.934; Ncor=0.856; logoDP=0.346; NsEucl=0.952; NSW=0.975; rcor=25; rNcor=2; rlogoDP=107; rNsEucl=13; rNSW=17; rank_mean=32.800; match_rank=20 a 0 0 0 0 0 0 0 0 0 0 29 47 3 100 0 0 0 0 12 25 33 0 0 c 0 0 0 0 0 0 0 0 0 0 21 19 73 0 100 0 0 7 4 39 23 0 0 g 0 0 0 0 0 0 0 0 0 0 29 7 22 0 0 100 0 93 64 18 22 0 0 t 0 0 0 0 0 0 0 0 0 0 21 27 2 0 0 0 100 0 20 18 22 0 0
AT4G18890_MA1333.1_JASPAR_shift10 (AT4G18890:MA1333.1:JASPAR)	0.900	0.825	7.605	0.934	0.953	56	4	9	48	54	34.200	22	; oligos_5-8nt_m1 versus AT4G18890_MA1333.1_JASPAR (AT4G18890:MA1333.1:JASPAR); m=22/125; ncol2=11; w=11; offset=1; strand=D; shift=10; score= 34.2; ----------yrCACGTGTgr-- ; cor=0.900; Ncor=0.825; logoDP=7.605; NsEucl=0.934; NSW=0.953; rcor=56; rNcor=4; rlogoDP=9; rNsEucl=48; rNSW=54; rank_mean=34.200; match_rank=22 a 0 0 0 0 0 0 0 0 0 0 3 179 0 590 0 1 1 0 51 60 239 0 0 c 0 0 0 0 0 0 0 0 0 0 319 28 589 0 590 0 0 0 74 140 91 0 0 g 0 0 0 0 0 0 0 0 0 0 43 383 0 0 0 589 0 590 60 338 179 0 0 t 0 0 0 0 0 0 0 0 0 0 225 0 1 0 0 0 589 0 405 52 81 0 0