One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.150715_JPTZeZ/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_2019-07-04.150715_JPTZeZ/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m2_shift9 ; 123 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_shift9 (oligos_5-8nt_m2)
; oligos_5-8nt_m2; m=0 (reference); ncol1=14; shift=9; ncol=23; ---------twgACACGTGgswd ; Alignment reference a 0 0 0 0 0 0 0 0 0 54 71 40 174 13 234 13 11 10 11 33 43 73 70 c 0 0 0 0 0 0 0 0 0 51 47 41 31 215 2 216 1 6 9 22 64 58 43 g 0 0 0 0 0 0 0 0 0 63 59 134 20 8 10 11 231 4 224 145 114 54 67 t 0 0 0 0 0 0 0 0 0 85 76 38 28 17 7 13 10 233 9 53 32 68 73

BZR1_MA0550.1_JASPAR_rc_shift9 (BZR1:MA0550.1:JASPAR_rc) 0.927 0.927 6.336 0.958 0.976 23 1 31 9 15 15.800 3
; oligos_5-8nt_m2 versus BZR1_MA0550.1_JASPAR_rc (BZR1:MA0550.1:JASPAR_rc); m=3/122; ncol2=14; w=14; offset=0; strand=R; shift=9; score= 15.8; ---------kkbhCACGTGkmkk ; cor=0.927; Ncor=0.927; logoDP=6.336; NsEucl=0.958; NSW=0.976; rcor=23; rNcor=1; rlogoDP=31; rNsEucl=9; rNSW=15; rank_mean=15.800; match_rank=3 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

ATAREB1_M0256_1.02_CISBP_shift8 (ATAREB1:M0256_1.02:CISBP) 0.948 0.758 4.900 0.963 0.983 10 3 63 1 5 16.400 4
; oligos_5-8nt_m2 versus ATAREB1_M0256_1.02_CISBP (ATAREB1:M0256_1.02:CISBP); m=4/122; ncol2=13; w=12; offset=-1; strand=D; shift=8; score= 16.4; --------cayrACACGTgkt-- ; cor=0.948; Ncor=0.758; logoDP=4.900; NsEucl=0.963; NSW=0.983; rcor=10; rNcor=3; rlogoDP=63; rNsEucl=1; rNSW=5; rank_mean=16.400; match_rank=4 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

ABF2_MA0941.1_JASPAR_shift8 (ABF2:MA0941.1:JASPAR) 0.947 0.758 4.927 0.963 0.983 11 4 62 2 6 17.000 5
; oligos_5-8nt_m2 versus ABF2_MA0941.1_JASPAR (ABF2:MA0941.1:JASPAR); m=5/122; ncol2=13; w=12; offset=-1; strand=D; shift=8; score= 17; --------cayrACACGTgkt-- ; cor=0.947; Ncor=0.758; logoDP=4.927; NsEucl=0.963; NSW=0.983; rcor=11; rNcor=4; rlogoDP=62; rNsEucl=2; rNSW=6; rank_mean=17.000; match_rank=5 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

HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR) 0.883 0.772 6.464 0.941 0.951 65 2 24 26 61 35.600 17
; oligos_5-8nt_m2 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=17/122; ncol2=16; w=14; offset=-1; strand=D; shift=8; score= 35.6; --------wwtGmCACGTGkCaw ; cor=0.883; Ncor=0.772; logoDP=6.464; NsEucl=0.941; NSW=0.951; rcor=65; rNcor=2; rlogoDP=24; rNsEucl=26; rNSW=61; rank_mean=35.600; match_rank=17 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_m2_shift9 (oligos_5-8nt_m2)													; oligos_5-8nt_m2; m=0 (reference); ncol1=14; shift=9; ncol=23; ---------twgACACGTGgswd ; Alignment reference a 0 0 0 0 0 0 0 0 0 54 71 40 174 13 234 13 11 10 11 33 43 73 70 c 0 0 0 0 0 0 0 0 0 51 47 41 31 215 2 216 1 6 9 22 64 58 43 g 0 0 0 0 0 0 0 0 0 63 59 134 20 8 10 11 231 4 224 145 114 54 67 t 0 0 0 0 0 0 0 0 0 85 76 38 28 17 7 13 10 233 9 53 32 68 73
BZR1_MA0550.1_JASPAR_rc_shift9 (BZR1:MA0550.1:JASPAR_rc)	0.927	0.927	6.336	0.958	0.976	23	1	31	9	15	15.800	3	; oligos_5-8nt_m2 versus BZR1_MA0550.1_JASPAR_rc (BZR1:MA0550.1:JASPAR_rc); m=3/122; ncol2=14; w=14; offset=0; strand=R; shift=9; score= 15.8; ---------kkbhCACGTGkmkk ; cor=0.927; Ncor=0.927; logoDP=6.336; NsEucl=0.958; NSW=0.976; rcor=23; rNcor=1; rlogoDP=31; rNsEucl=9; rNSW=15; rank_mean=15.800; match_rank=3 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
ATAREB1_M0256_1.02_CISBP_shift8 (ATAREB1:M0256_1.02:CISBP)	0.948	0.758	4.900	0.963	0.983	10	3	63	1	5	16.400	4	; oligos_5-8nt_m2 versus ATAREB1_M0256_1.02_CISBP (ATAREB1:M0256_1.02:CISBP); m=4/122; ncol2=13; w=12; offset=-1; strand=D; shift=8; score= 16.4; --------cayrACACGTgkt-- ; cor=0.948; Ncor=0.758; logoDP=4.900; NsEucl=0.963; NSW=0.983; rcor=10; rNcor=3; rlogoDP=63; rNsEucl=1; rNSW=5; rank_mean=16.400; match_rank=4 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
ABF2_MA0941.1_JASPAR_shift8 (ABF2:MA0941.1:JASPAR)	0.947	0.758	4.927	0.963	0.983	11	4	62	2	6	17.000	5	; oligos_5-8nt_m2 versus ABF2_MA0941.1_JASPAR (ABF2:MA0941.1:JASPAR); m=5/122; ncol2=13; w=12; offset=-1; strand=D; shift=8; score= 17; --------cayrACACGTgkt-- ; cor=0.947; Ncor=0.758; logoDP=4.927; NsEucl=0.963; NSW=0.983; rcor=11; rNcor=4; rlogoDP=62; rNsEucl=2; rNSW=6; rank_mean=17.000; match_rank=5 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
HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR)	0.883	0.772	6.464	0.941	0.951	65	2	24	26	61	35.600	17	; oligos_5-8nt_m2 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=17/122; ncol2=16; w=14; offset=-1; strand=D; shift=8; score= 35.6; --------wwtGmCACGTGkCaw ; cor=0.883; Ncor=0.772; logoDP=6.464; NsEucl=0.941; NSW=0.951; rcor=65; rNcor=2; rlogoDP=24; rNsEucl=26; rNSW=61; rank_mean=35.600; match_rank=17 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