One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/02/compare-matrices_2019-07-02.163714_0n17GM/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_2019-07-02.163714_0n17GM/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=12; shift=9; ncol=23; ---------dmaCACGTGtkm-- ; Alignment reference a 0 0 0 0 0 0 0 0 0 49 52 121 4 173 5 5 5 12 34 44 50 0 0 c 0 0 0 0 0 0 0 0 0 44 48 22 156 3 175 3 7 11 15 45 47 0 0 g 0 0 0 0 0 0 0 0 0 48 42 14 13 7 3 175 2 161 20 47 45 0 0 t 0 0 0 0 0 0 0 0 0 47 46 31 15 5 5 5 174 4 119 52 46 0 0

BES1_MA0549.1_JASPAR_shift10 (BES1:MA0549.1:JASPAR) 0.923 0.846 6.745 0.946 0.968 22 2 29 19 25 19.400 3
; oligos_5-8nt_m1 versus BES1_MA0549.1_JASPAR (BES1:MA0549.1:JASPAR); m=3/124; ncol2=11; w=11; offset=1; strand=D; shift=10; score= 19.4; ----------crCACGTGksv-- ; cor=0.923; Ncor=0.846; logoDP=6.745; NsEucl=0.946; NSW=0.968; rcor=22; rNcor=2; rlogoDP=29; rNsEucl=19; rNSW=25; rank_mean=19.400; match_rank=3 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_shift9 (ABF1:M0257_1.02:CISBP) 0.939 0.861 3.660 0.956 0.979 13 1 78 5 6 20.600 7
; oligos_5-8nt_m1 versus ABF1_M0257_1.02_CISBP (ABF1:M0257_1.02:CISBP); m=7/124; ncol2=11; w=11; offset=0; strand=D; shift=9; score= 20.6; ---------gdACACGTGkb--- ; cor=0.939; Ncor=0.861; logoDP=3.660; NsEucl=0.956; NSW=0.979; rcor=13; rNcor=1; rlogoDP=78; rNsEucl=5; rNSW=6; rank_mean=20.600; match_rank=7 a 0 0 0 0 0 0 0 0 0 21 26 68 16 73 0 18 0 12 16 18 0 0 0 c 0 0 0 0 0 0 0 0 0 21 16 18 75 8 91 0 10 4 19 28 0 0 0 g 0 0 0 0 0 0 0 0 0 37 33 7 0 10 0 82 0 71 40 28 0 0 0 t 0 0 0 0 0 0 0 0 0 21 25 7 9 9 9 0 90 13 25 26 0 0 0

AT4G18890_MA1333.1_JASPAR_shift10 (AT4G18890:MA1333.1:JASPAR) 0.907 0.831 7.337 0.936 0.955 38 4 7 43 48 28.000 10
; oligos_5-8nt_m1 versus AT4G18890_MA1333.1_JASPAR (AT4G18890:MA1333.1:JASPAR); m=10/124; ncol2=11; w=11; offset=1; strand=D; shift=10; score= 28; ----------yrCACGTGTgr-- ; cor=0.907; Ncor=0.831; logoDP=7.337; NsEucl=0.936; NSW=0.955; rcor=38; rNcor=4; rlogoDP=7; rNsEucl=43; rNSW=48; rank_mean=28.000; match_rank=10 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

LOC_Os02g49560_M0327_1.02_CISBP_rc_shift10 (LOC_Os02g49560:M0327_1.02:CISBP_rc) 0.921 0.845 0.319 0.948 0.970 23 3 109 12 19 33.200 18
; oligos_5-8nt_m1 versus LOC_Os02g49560_M0327_1.02_CISBP_rc (LOC_Os02g49560:M0327_1.02:CISBP_rc); m=18/124; ncol2=11; w=11; offset=1; strand=R; shift=10; score= 33.2; ----------rwCACGTGgma-- ; cor=0.921; Ncor=0.845; logoDP=0.319; NsEucl=0.948; NSW=0.970; rcor=23; rNcor=3; rlogoDP=109; rNsEucl=12; rNSW=19; rank_mean=33.200; match_rank=18 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

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; ---------dmaCACGTGtkm-- ; Alignment reference a 0 0 0 0 0 0 0 0 0 49 52 121 4 173 5 5 5 12 34 44 50 0 0 c 0 0 0 0 0 0 0 0 0 44 48 22 156 3 175 3 7 11 15 45 47 0 0 g 0 0 0 0 0 0 0 0 0 48 42 14 13 7 3 175 2 161 20 47 45 0 0 t 0 0 0 0 0 0 0 0 0 47 46 31 15 5 5 5 174 4 119 52 46 0 0
BES1_MA0549.1_JASPAR_shift10 (BES1:MA0549.1:JASPAR)	0.923	0.846	6.745	0.946	0.968	22	2	29	19	25	19.400	3	; oligos_5-8nt_m1 versus BES1_MA0549.1_JASPAR (BES1:MA0549.1:JASPAR); m=3/124; ncol2=11; w=11; offset=1; strand=D; shift=10; score= 19.4; ----------crCACGTGksv-- ; cor=0.923; Ncor=0.846; logoDP=6.745; NsEucl=0.946; NSW=0.968; rcor=22; rNcor=2; rlogoDP=29; rNsEucl=19; rNSW=25; rank_mean=19.400; match_rank=3 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_shift9 (ABF1:M0257_1.02:CISBP)	0.939	0.861	3.660	0.956	0.979	13	1	78	5	6	20.600	7	; oligos_5-8nt_m1 versus ABF1_M0257_1.02_CISBP (ABF1:M0257_1.02:CISBP); m=7/124; ncol2=11; w=11; offset=0; strand=D; shift=9; score= 20.6; ---------gdACACGTGkb--- ; cor=0.939; Ncor=0.861; logoDP=3.660; NsEucl=0.956; NSW=0.979; rcor=13; rNcor=1; rlogoDP=78; rNsEucl=5; rNSW=6; rank_mean=20.600; match_rank=7 a 0 0 0 0 0 0 0 0 0 21 26 68 16 73 0 18 0 12 16 18 0 0 0 c 0 0 0 0 0 0 0 0 0 21 16 18 75 8 91 0 10 4 19 28 0 0 0 g 0 0 0 0 0 0 0 0 0 37 33 7 0 10 0 82 0 71 40 28 0 0 0 t 0 0 0 0 0 0 0 0 0 21 25 7 9 9 9 0 90 13 25 26 0 0 0
AT4G18890_MA1333.1_JASPAR_shift10 (AT4G18890:MA1333.1:JASPAR)	0.907	0.831	7.337	0.936	0.955	38	4	7	43	48	28.000	10	; oligos_5-8nt_m1 versus AT4G18890_MA1333.1_JASPAR (AT4G18890:MA1333.1:JASPAR); m=10/124; ncol2=11; w=11; offset=1; strand=D; shift=10; score= 28; ----------yrCACGTGTgr-- ; cor=0.907; Ncor=0.831; logoDP=7.337; NsEucl=0.936; NSW=0.955; rcor=38; rNcor=4; rlogoDP=7; rNsEucl=43; rNSW=48; rank_mean=28.000; match_rank=10 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
LOC_Os02g49560_M0327_1.02_CISBP_rc_shift10 (LOC_Os02g49560:M0327_1.02:CISBP_rc)	0.921	0.845	0.319	0.948	0.970	23	3	109	12	19	33.200	18	; oligos_5-8nt_m1 versus LOC_Os02g49560_M0327_1.02_CISBP_rc (LOC_Os02g49560:M0327_1.02:CISBP_rc); m=18/124; ncol2=11; w=11; offset=1; strand=R; shift=10; score= 33.2; ----------rwCACGTGgma-- ; cor=0.921; Ncor=0.845; logoDP=0.319; NsEucl=0.948; NSW=0.970; rcor=23; rNcor=3; rlogoDP=109; rNsEucl=12; rNSW=19; rank_mean=33.200; match_rank=18 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