One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/03/compare-matrices_2019-07-03.165213_cYFzkB/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/2019/07/03/compare-matrices_2019-07-03.165213_cYFzkB/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m3_shift8 ; 151 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_m3_shift8 (oligos_5-8nt_m3)
; oligos_5-8nt_m3; m=0 (reference); ncol1=15; shift=8; ncol=29; --------wwGAAAAGTCAAAaw------ ; Alignment reference a 0 0 0 0 0 0 0 0 125 113 46 272 310 298 308 23 27 21 269 267 238 114 114 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 57 49 19 20 12 7 11 10 12 285 20 16 28 61 64 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 58 60 252 18 10 15 4 285 9 11 19 25 31 85 71 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 101 119 24 31 9 21 18 23 293 24 33 33 44 81 92 0 0 0 0 0 0

WRKY40.ampDAP_M0835_AthalianaCistrome_shift9 (WRKY40.ampDAP:M0835:AthalianaCistrome) 0.873 0.757 5.566 0.939 0.951 15 4 14 6 7 9.200 3
; oligos_5-8nt_m3 versus WRKY40.ampDAP_M0835_AthalianaCistrome (WRKY40.ampDAP:M0835:AthalianaCistrome); m=3/150; ncol2=13; w=13; offset=1; strand=D; shift=9; score= 9.2; ---------raaAAAGTCAAmr------- ; cor=0.873; Ncor=0.757; logoDP=5.566; NsEucl=0.939; NSW=0.951; rcor=15; rNcor=4; rlogoDP=14; rNsEucl=6; rNSW=7; rank_mean=9.200; match_rank=3 a 0 0 0 0 0 0 0 0 0 190 231 291 385 421 477 0 0 0 561 561 150 196 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 105 83 111 84 43 0 0 5 561 0 0 281 75 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 146 126 87 47 12 84 561 0 0 0 0 82 241 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 120 121 72 45 85 0 0 556 0 0 0 48 49 0 0 0 0 0 0 0

WRKY50_MA1317.1_JASPAR_rc_shift9 (WRKY50:MA1317.1:JASPAR_rc) 0.919 0.797 2.475 0.948 0.964 3 2 87 2 2 19.200 7
; oligos_5-8nt_m3 versus WRKY50_MA1317.1_JASPAR_rc (WRKY50:MA1317.1:JASPAR_rc); m=7/150; ncol2=13; w=13; offset=1; strand=R; shift=9; score= 19.2; ---------waAAAAGTCAAmr------- ; cor=0.919; Ncor=0.797; logoDP=2.475; NsEucl=0.948; NSW=0.964; rcor=3; rNcor=2; rlogoDP=87; rNsEucl=2; rNSW=2; rank_mean=19.200; match_rank=7 a 0 0 0 0 0 0 0 0 0 215 274 406 502 511 543 0 0 0 565 559 239 163 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 87 90 48 14 4 1 0 1 568 0 2 216 88 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 124 88 63 23 10 22 568 0 0 0 1 56 213 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 142 116 51 29 43 2 0 567 0 3 6 57 104 0 0 0 0 0 0 0

WRKY40.DAP_M0812_AthalianaCistrome_rc_shift9 (WRKY40.DAP:M0812:AthalianaCistrome_rc) 0.866 0.758 2.213 0.942 0.953 22 3 97 3 6 26.200 16
; oligos_5-8nt_m3 versus WRKY40.DAP_M0812_AthalianaCistrome_rc (WRKY40.DAP:M0812:AthalianaCistrome_rc); m=16/150; ncol2=15; w=14; offset=1; strand=R; shift=9; score= 26.2; ---------raaaAAGTCAAmrwh----- ; cor=0.866; Ncor=0.758; logoDP=2.213; NsEucl=0.942; NSW=0.953; rcor=22; rNcor=3; rlogoDP=97; rNsEucl=3; rNSW=6; rank_mean=26.200; match_rank=16 a 0 0 0 0 0 0 0 0 0 190 249 315 399 433 475 0 0 1 600 594 161 171 165 166 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 98 82 129 97 40 0 0 3 599 0 0 279 77 125 173 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 163 131 90 37 19 125 600 0 0 0 0 89 291 136 69 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 149 138 66 67 108 0 0 597 0 0 6 71 61 174 192 0 0 0 0 0

WRKY43.ampDAP_M0828_AthalianaCistrome_shift8 (WRKY43.ampDAP:M0828:AthalianaCistrome) 0.803 0.803 5.563 0.931 0.929 60 1 15 16 41 26.600 17
; oligos_5-8nt_m3 versus WRKY43.ampDAP_M0828_AthalianaCistrome (WRKY43.ampDAP:M0828:AthalianaCistrome); m=17/150; ncol2=15; w=15; offset=0; strand=D; shift=8; score= 26.6; --------waaaAAAGTCAACGm------ ; cor=0.803; Ncor=0.803; logoDP=5.563; NsEucl=0.931; NSW=0.929; rcor=60; rNcor=1; rlogoDP=15; rNsEucl=16; rNSW=41; rank_mean=26.600; match_rank=17 a 0 0 0 0 0 0 0 0 242 225 251 321 423 423 467 0 0 0 589 589 71 83 188 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 119 104 110 89 33 41 0 0 0 589 0 0 498 42 160 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 75 125 115 88 42 21 122 589 0 0 0 0 0 419 118 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 153 135 113 91 91 104 0 0 589 0 0 0 20 45 123 0 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m3_shift8 (oligos_5-8nt_m3)													; oligos_5-8nt_m3; m=0 (reference); ncol1=15; shift=8; ncol=29; --------wwGAAAAGTCAAAaw------ ; Alignment reference a 0 0 0 0 0 0 0 0 125 113 46 272 310 298 308 23 27 21 269 267 238 114 114 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 57 49 19 20 12 7 11 10 12 285 20 16 28 61 64 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 58 60 252 18 10 15 4 285 9 11 19 25 31 85 71 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 101 119 24 31 9 21 18 23 293 24 33 33 44 81 92 0 0 0 0 0 0
WRKY40.ampDAP_M0835_AthalianaCistrome_shift9 (WRKY40.ampDAP:M0835:AthalianaCistrome)	0.873	0.757	5.566	0.939	0.951	15	4	14	6	7	9.200	3	; oligos_5-8nt_m3 versus WRKY40.ampDAP_M0835_AthalianaCistrome (WRKY40.ampDAP:M0835:AthalianaCistrome); m=3/150; ncol2=13; w=13; offset=1; strand=D; shift=9; score= 9.2; ---------raaAAAGTCAAmr------- ; cor=0.873; Ncor=0.757; logoDP=5.566; NsEucl=0.939; NSW=0.951; rcor=15; rNcor=4; rlogoDP=14; rNsEucl=6; rNSW=7; rank_mean=9.200; match_rank=3 a 0 0 0 0 0 0 0 0 0 190 231 291 385 421 477 0 0 0 561 561 150 196 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 105 83 111 84 43 0 0 5 561 0 0 281 75 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 146 126 87 47 12 84 561 0 0 0 0 82 241 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 120 121 72 45 85 0 0 556 0 0 0 48 49 0 0 0 0 0 0 0
WRKY50_MA1317.1_JASPAR_rc_shift9 (WRKY50:MA1317.1:JASPAR_rc)	0.919	0.797	2.475	0.948	0.964	3	2	87	2	2	19.200	7	; oligos_5-8nt_m3 versus WRKY50_MA1317.1_JASPAR_rc (WRKY50:MA1317.1:JASPAR_rc); m=7/150; ncol2=13; w=13; offset=1; strand=R; shift=9; score= 19.2; ---------waAAAAGTCAAmr------- ; cor=0.919; Ncor=0.797; logoDP=2.475; NsEucl=0.948; NSW=0.964; rcor=3; rNcor=2; rlogoDP=87; rNsEucl=2; rNSW=2; rank_mean=19.200; match_rank=7 a 0 0 0 0 0 0 0 0 0 215 274 406 502 511 543 0 0 0 565 559 239 163 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 87 90 48 14 4 1 0 1 568 0 2 216 88 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 124 88 63 23 10 22 568 0 0 0 1 56 213 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 142 116 51 29 43 2 0 567 0 3 6 57 104 0 0 0 0 0 0 0
WRKY40.DAP_M0812_AthalianaCistrome_rc_shift9 (WRKY40.DAP:M0812:AthalianaCistrome_rc)	0.866	0.758	2.213	0.942	0.953	22	3	97	3	6	26.200	16	; oligos_5-8nt_m3 versus WRKY40.DAP_M0812_AthalianaCistrome_rc (WRKY40.DAP:M0812:AthalianaCistrome_rc); m=16/150; ncol2=15; w=14; offset=1; strand=R; shift=9; score= 26.2; ---------raaaAAGTCAAmrwh----- ; cor=0.866; Ncor=0.758; logoDP=2.213; NsEucl=0.942; NSW=0.953; rcor=22; rNcor=3; rlogoDP=97; rNsEucl=3; rNSW=6; rank_mean=26.200; match_rank=16 a 0 0 0 0 0 0 0 0 0 190 249 315 399 433 475 0 0 1 600 594 161 171 165 166 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 98 82 129 97 40 0 0 3 599 0 0 279 77 125 173 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 163 131 90 37 19 125 600 0 0 0 0 89 291 136 69 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 149 138 66 67 108 0 0 597 0 0 6 71 61 174 192 0 0 0 0 0
WRKY43.ampDAP_M0828_AthalianaCistrome_shift8 (WRKY43.ampDAP:M0828:AthalianaCistrome)	0.803	0.803	5.563	0.931	0.929	60	1	15	16	41	26.600	17	; oligos_5-8nt_m3 versus WRKY43.ampDAP_M0828_AthalianaCistrome (WRKY43.ampDAP:M0828:AthalianaCistrome); m=17/150; ncol2=15; w=15; offset=0; strand=D; shift=8; score= 26.6; --------waaaAAAGTCAACGm------ ; cor=0.803; Ncor=0.803; logoDP=5.563; NsEucl=0.931; NSW=0.929; rcor=60; rNcor=1; rlogoDP=15; rNsEucl=16; rNSW=41; rank_mean=26.600; match_rank=17 a 0 0 0 0 0 0 0 0 242 225 251 321 423 423 467 0 0 0 589 589 71 83 188 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 119 104 110 89 33 41 0 0 0 589 0 0 498 42 160 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 75 125 115 88 42 21 122 589 0 0 0 0 0 419 118 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 153 135 113 91 91 104 0 0 589 0 0 0 20 45 123 0 0 0 0 0 0