One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.144811_MtHtt5/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_2019-07-04.144811_MtHtt5/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift9 ; 120 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 0 133 126 97 324 19 433 25 23 19 27 53 92 153 143 c 0 0 0 0 0 0 0 0 0 93 93 81 64 411 6 415 7 12 10 27 197 98 99 g 0 0 0 0 0 0 0 0 0 100 97 203 27 11 11 7 415 7 415 65 81 91 94 t 0 0 0 0 0 0 0 0 0 144 154 89 55 29 20 23 25 432 18 325 100 128 134

ABF2_MA0941.1_JASPAR_shift8 (ABF2:MA0941.1:JASPAR) 0.956 0.765 4.952 0.966 0.986 5 3 57 1 1 13.400 1
; oligos_5-8nt_m1 versus ABF2_MA0941.1_JASPAR (ABF2:MA0941.1:JASPAR); m=1/119; ncol2=13; w=12; offset=-1; strand=D; shift=8; score= 13.4; --------cayrACACGTgkt-- ; cor=0.956; Ncor=0.765; logoDP=4.952; NsEucl=0.966; NSW=0.986; rcor=5; rNcor=3; rlogoDP=57; rNsEucl=1; rNSW=1; rank_mean=13.400; 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

BZR1_MA0550.1_JASPAR_rc_shift9 (BZR1:MA0550.1:JASPAR_rc) 0.913 0.913 6.411 0.955 0.972 21 1 26 7 16 14.200 2
; oligos_5-8nt_m1 versus BZR1_MA0550.1_JASPAR_rc (BZR1:MA0550.1:JASPAR_rc); m=2/119; ncol2=14; w=14; offset=0; strand=R; shift=9; score= 14.2; ---------kkbhCACGTGkmkk ; cor=0.913; Ncor=0.913; logoDP=6.411; NsEucl=0.955; NSW=0.972; rcor=21; rNcor=1; rlogoDP=26; rNsEucl=7; rNSW=16; rank_mean=14.200; match_rank=2 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) 0.956 0.765 4.928 0.965 0.986 6 4 58 2 2 14.400 3
; oligos_5-8nt_m1 versus ATAREB1_M0256_1.02_CISBP (ATAREB1:M0256_1.02:CISBP); m=3/119; ncol2=13; w=12; offset=-1; strand=D; shift=8; score= 14.4; --------cayrACACGTgkt-- ; cor=0.956; Ncor=0.765; logoDP=4.928; NsEucl=0.965; NSW=0.986; rcor=6; rNcor=4; rlogoDP=58; rNsEucl=2; rNSW=2; rank_mean=14.400; match_rank=3 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

HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR) 0.901 0.788 6.531 0.945 0.957 30 2 24 20 34 22.000 11
; oligos_5-8nt_m1 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=11/119; ncol2=16; w=14; offset=-1; strand=D; shift=8; score= 22; --------wwtGmCACGTGkCaw ; cor=0.901; Ncor=0.788; logoDP=6.531; NsEucl=0.945; NSW=0.957; rcor=30; rNcor=2; rlogoDP=24; rNsEucl=20; rNSW=34; rank_mean=22.000; match_rank=11 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 0 133 126 97 324 19 433 25 23 19 27 53 92 153 143 c 0 0 0 0 0 0 0 0 0 93 93 81 64 411 6 415 7 12 10 27 197 98 99 g 0 0 0 0 0 0 0 0 0 100 97 203 27 11 11 7 415 7 415 65 81 91 94 t 0 0 0 0 0 0 0 0 0 144 154 89 55 29 20 23 25 432 18 325 100 128 134
ABF2_MA0941.1_JASPAR_shift8 (ABF2:MA0941.1:JASPAR)	0.956	0.765	4.952	0.966	0.986	5	3	57	1	1	13.400	1	; oligos_5-8nt_m1 versus ABF2_MA0941.1_JASPAR (ABF2:MA0941.1:JASPAR); m=1/119; ncol2=13; w=12; offset=-1; strand=D; shift=8; score= 13.4; --------cayrACACGTgkt-- ; cor=0.956; Ncor=0.765; logoDP=4.952; NsEucl=0.966; NSW=0.986; rcor=5; rNcor=3; rlogoDP=57; rNsEucl=1; rNSW=1; rank_mean=13.400; 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
BZR1_MA0550.1_JASPAR_rc_shift9 (BZR1:MA0550.1:JASPAR_rc)	0.913	0.913	6.411	0.955	0.972	21	1	26	7	16	14.200	2	; oligos_5-8nt_m1 versus BZR1_MA0550.1_JASPAR_rc (BZR1:MA0550.1:JASPAR_rc); m=2/119; ncol2=14; w=14; offset=0; strand=R; shift=9; score= 14.2; ---------kkbhCACGTGkmkk ; cor=0.913; Ncor=0.913; logoDP=6.411; NsEucl=0.955; NSW=0.972; rcor=21; rNcor=1; rlogoDP=26; rNsEucl=7; rNSW=16; rank_mean=14.200; match_rank=2 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)	0.956	0.765	4.928	0.965	0.986	6	4	58	2	2	14.400	3	; oligos_5-8nt_m1 versus ATAREB1_M0256_1.02_CISBP (ATAREB1:M0256_1.02:CISBP); m=3/119; ncol2=13; w=12; offset=-1; strand=D; shift=8; score= 14.4; --------cayrACACGTgkt-- ; cor=0.956; Ncor=0.765; logoDP=4.928; NsEucl=0.965; NSW=0.986; rcor=6; rNcor=4; rlogoDP=58; rNsEucl=2; rNSW=2; rank_mean=14.400; match_rank=3 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
HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR)	0.901	0.788	6.531	0.945	0.957	30	2	24	20	34	22.000	11	; oligos_5-8nt_m1 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=11/119; ncol2=16; w=14; offset=-1; strand=D; shift=8; score= 22; --------wwtGmCACGTGkCaw ; cor=0.901; Ncor=0.788; logoDP=6.531; NsEucl=0.945; NSW=0.957; rcor=30; rNcor=2; rlogoDP=24; rNsEucl=20; rNSW=34; rank_mean=22.000; match_rank=11 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