One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/03/compare-matrices_2019-07-03.165939_hs6pby/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_2019-07-03.165939_hs6pby/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_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_m1_shift8 (oligos_5-8nt_m1)
; oligos_5-8nt_m1; m=0 (reference); ncol1=15; shift=8; ncol=29; --------wwGAAAAGTCAAAaw------ ; Alignment reference a 0 0 0 0 0 0 0 0 101 97 37 219 251 241 248 19 26 18 213 213 191 91 92 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 41 41 17 17 9 7 7 4 9 232 19 10 21 47 44 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 45 36 200 13 5 10 4 233 3 8 13 23 27 68 61 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 87 100 20 25 9 16 15 18 236 16 29 28 35 68 77 0 0 0 0 0 0

WRKY40.ampDAP_M0835_AthalianaCistrome_shift9 (WRKY40.ampDAP:M0835:AthalianaCistrome) 0.872 0.756 5.707 0.938 0.950 16 4 14 6 7 9.400 3
; oligos_5-8nt_m1 versus WRKY40.ampDAP_M0835_AthalianaCistrome (WRKY40.ampDAP:M0835:AthalianaCistrome); m=3/150; ncol2=13; w=13; offset=1; strand=D; shift=9; score= 9.4; ---------raaAAAGTCAAmr------- ; cor=0.872; Ncor=0.756; logoDP=5.707; NsEucl=0.938; NSW=0.950; rcor=16; rNcor=4; rlogoDP=14; rNsEucl=6; rNSW=7; rank_mean=9.400; 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 2.500 0.948 0.964 3 2 89 2 2 19.600 7
; oligos_5-8nt_m1 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= 19.6; ---------waAAAAGTCAAmr------- ; cor=0.919; Ncor=0.797; logoDP=2.500; NsEucl=0.948; NSW=0.964; rcor=3; rNcor=2; rlogoDP=89; rNsEucl=2; rNSW=2; rank_mean=19.600; 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) 0.865 0.757 2.365 0.941 0.952 23 3 95 3 6 26.000 16
; oligos_5-8nt_m1 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; ---------raaaAAGTCAAmrwh----- ; cor=0.865; Ncor=0.757; logoDP=2.365; NsEucl=0.941; NSW=0.952; rcor=23; rNcor=3; rlogoDP=95; rNsEucl=3; rNSW=6; rank_mean=26.000; 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) 0.802 0.802 5.706 0.931 0.928 61 1 15 16 42 27.000 17
; oligos_5-8nt_m1 versus WRKY43.ampDAP_M0828_AthalianaCistrome (WRKY43.ampDAP:M0828:AthalianaCistrome); m=17/150; ncol2=15; w=15; offset=0; strand=D; shift=8; score= 27; --------waaaAAAGTCAACGm------ ; cor=0.802; Ncor=0.802; logoDP=5.706; NsEucl=0.931; NSW=0.928; rcor=61; rNcor=1; rlogoDP=15; rNsEucl=16; rNSW=42; rank_mean=27.000; 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_m1_shift8 (oligos_5-8nt_m1)													; oligos_5-8nt_m1; m=0 (reference); ncol1=15; shift=8; ncol=29; --------wwGAAAAGTCAAAaw------ ; Alignment reference a 0 0 0 0 0 0 0 0 101 97 37 219 251 241 248 19 26 18 213 213 191 91 92 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 41 41 17 17 9 7 7 4 9 232 19 10 21 47 44 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 45 36 200 13 5 10 4 233 3 8 13 23 27 68 61 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 87 100 20 25 9 16 15 18 236 16 29 28 35 68 77 0 0 0 0 0 0
WRKY40.ampDAP_M0835_AthalianaCistrome_shift9 (WRKY40.ampDAP:M0835:AthalianaCistrome)	0.872	0.756	5.707	0.938	0.950	16	4	14	6	7	9.400	3	; oligos_5-8nt_m1 versus WRKY40.ampDAP_M0835_AthalianaCistrome (WRKY40.ampDAP:M0835:AthalianaCistrome); m=3/150; ncol2=13; w=13; offset=1; strand=D; shift=9; score= 9.4; ---------raaAAAGTCAAmr------- ; cor=0.872; Ncor=0.756; logoDP=5.707; NsEucl=0.938; NSW=0.950; rcor=16; rNcor=4; rlogoDP=14; rNsEucl=6; rNSW=7; rank_mean=9.400; 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	2.500	0.948	0.964	3	2	89	2	2	19.600	7	; oligos_5-8nt_m1 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= 19.6; ---------waAAAAGTCAAmr------- ; cor=0.919; Ncor=0.797; logoDP=2.500; NsEucl=0.948; NSW=0.964; rcor=3; rNcor=2; rlogoDP=89; rNsEucl=2; rNSW=2; rank_mean=19.600; 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)	0.865	0.757	2.365	0.941	0.952	23	3	95	3	6	26.000	16	; oligos_5-8nt_m1 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; ---------raaaAAGTCAAmrwh----- ; cor=0.865; Ncor=0.757; logoDP=2.365; NsEucl=0.941; NSW=0.952; rcor=23; rNcor=3; rlogoDP=95; rNsEucl=3; rNSW=6; rank_mean=26.000; 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)	0.802	0.802	5.706	0.931	0.928	61	1	15	16	42	27.000	17	; oligos_5-8nt_m1 versus WRKY43.ampDAP_M0828_AthalianaCistrome (WRKY43.ampDAP:M0828:AthalianaCistrome); m=17/150; ncol2=15; w=15; offset=0; strand=D; shift=8; score= 27; --------waaaAAAGTCAACGm------ ; cor=0.802; Ncor=0.802; logoDP=5.706; NsEucl=0.931; NSW=0.928; rcor=61; rNcor=1; rlogoDP=15; rNsEucl=16; rNSW=42; rank_mean=27.000; 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