One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.170352_nTG4CO/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_2019-07-04.170352_nTG4CO/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift7 ; 86 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_shift7 (oligos_5-8nt_m1)
; oligos_5-8nt_m1; m=0 (reference); ncol1=18; shift=7; ncol=25; -------wvttGMCACGTGGCaabr ; Alignment reference a 0 0 0 0 0 0 0 25 27 19 18 4 26 3 96 6 6 0 4 2 14 53 39 19 27 c 0 0 0 0 0 0 0 24 25 20 18 6 69 87 2 84 4 2 5 3 76 11 21 27 24 g 0 0 0 0 0 0 0 24 28 22 12 76 3 6 2 4 85 2 88 71 6 18 19 26 25 t 0 0 0 0 0 0 0 27 20 39 52 14 2 4 0 6 5 96 3 24 4 18 21 28 24

HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR) 0.971 0.863 7.466 0.973 0.988 3 1 10 1 2 3.400 1
; oligos_5-8nt_m1 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=1/85; ncol2=16; w=16; offset=1; strand=D; shift=8; score= 3.4; --------wwtGmCACGTGkCaww- ; cor=0.971; Ncor=0.863; logoDP=7.466; NsEucl=0.973; NSW=0.988; rcor=3; rNcor=1; rlogoDP=10; rNsEucl=1; rNSW=2; rank_mean=3.400; match_rank=1 a 0 0 0 0 0 0 0 0 103 108 52 9 150 0 310 3 1 0 2 4 24 183 94 89 0 c 0 0 0 0 0 0 0 0 60 56 55 8 165 317 1 311 5 9 1 1 279 30 62 68 0 g 0 0 0 0 0 0 0 0 68 62 30 279 1 1 9 5 311 1 317 165 8 55 56 60 0 t 0 0 0 0 0 0 0 0 89 94 183 24 4 2 0 1 3 310 0 150 9 52 108 103 0

ABI5.DAP_M0201_AthalianaCistrome_shift6 (ABI5.DAP:M0201:AthalianaCistrome) 0.839 0.751 7.331 0.944 0.947 41 4 12 10 29 19.200 9
; oligos_5-8nt_m1 versus ABI5.DAP_M0201_AthalianaCistrome (ABI5.DAP:M0201:AthalianaCistrome); m=9/85; ncol2=18; w=17; offset=-1; strand=D; shift=6; score= 19.2; ------wdrwgrwsACGTGKCarw- ; cor=0.839; Ncor=0.751; logoDP=7.331; NsEucl=0.944; NSW=0.947; rcor=41; rNcor=4; rlogoDP=12; rNsEucl=10; rNSW=29; rank_mean=19.200; match_rank=9 a 0 0 0 0 0 0 241 217 224 161 44 157 198 0 595 0 0 0 0 0 27 394 151 190 0 c 0 0 0 0 0 0 71 59 80 39 19 119 92 289 0 595 0 0 0 0 568 50 124 117 0 g 0 0 0 0 0 0 131 167 158 98 400 296 0 294 0 0 595 0 595 446 0 123 174 87 0 t 0 0 0 0 0 0 152 152 133 297 132 23 305 12 0 0 0 595 0 149 0 28 146 201 0

PIF3_PIF3_2_Athamap_rc_shift7 (PIF3:PIF3_2:Athamap_rc) 0.870 0.821 2.117 0.948 0.955 25 2 63 8 17 23.000 15
; oligos_5-8nt_m1 versus PIF3_PIF3_2_Athamap_rc (PIF3:PIF3_2:Athamap_rc); m=15/85; ncol2=17; w=17; offset=0; strand=R; shift=7; score= 23; -------rsbkbCCACGTGGbyhy- ; cor=0.870; Ncor=0.821; logoDP=2.117; NsEucl=0.948; NSW=0.955; rcor=25; rNcor=2; rlogoDP=63; rNsEucl=8; rNSW=17; rank_mean=23.000; match_rank=15 a 0 0 0 0 0 0 0 11 6 0 2 2 0 0 32 0 0 0 0 0 0 7 9 6 0 c 0 0 0 0 0 0 0 6 11 8 0 11 32 32 0 32 0 0 0 5 13 13 10 9 0 g 0 0 0 0 0 0 0 11 8 13 15 10 0 0 0 0 32 0 32 26 11 2 4 2 0 t 0 0 0 0 0 0 0 4 7 11 15 9 0 0 0 0 0 32 0 1 8 10 9 15 0

PIF3_PIF3_1_Athamap_shift7 (PIF3:PIF3_1:Athamap) 0.795 0.795 7.516 0.940 0.935 65 3 8 22 43 28.200 22
; oligos_5-8nt_m1 versus PIF3_PIF3_1_Athamap (PIF3:PIF3_1:Athamap); m=22/85; ncol2=18; w=18; offset=0; strand=D; shift=7; score= 28.2; -------gkrggmCACGTGrmswCk ; cor=0.795; Ncor=0.795; logoDP=7.516; NsEucl=0.940; NSW=0.935; rcor=65; rNcor=3; rlogoDP=8; rNsEucl=22; rNSW=43; rank_mean=28.200; match_rank=22 a 0 0 0 0 0 0 0 2 5 11 6 5 11 0 27 0 0 0 0 11 9 3 11 4 4 c 0 0 0 0 0 0 0 5 1 2 0 3 11 27 0 27 0 0 0 2 12 9 6 19 2 g 0 0 0 0 0 0 0 15 10 12 17 17 5 0 0 0 27 0 27 13 6 13 0 4 9 t 0 0 0 0 0 0 0 5 11 2 4 2 0 0 0 0 0 27 0 1 0 2 10 0 12

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m1_shift7 (oligos_5-8nt_m1)													; oligos_5-8nt_m1; m=0 (reference); ncol1=18; shift=7; ncol=25; -------wvttGMCACGTGGCaabr ; Alignment reference a 0 0 0 0 0 0 0 25 27 19 18 4 26 3 96 6 6 0 4 2 14 53 39 19 27 c 0 0 0 0 0 0 0 24 25 20 18 6 69 87 2 84 4 2 5 3 76 11 21 27 24 g 0 0 0 0 0 0 0 24 28 22 12 76 3 6 2 4 85 2 88 71 6 18 19 26 25 t 0 0 0 0 0 0 0 27 20 39 52 14 2 4 0 6 5 96 3 24 4 18 21 28 24
HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR)	0.971	0.863	7.466	0.973	0.988	3	1	10	1	2	3.400	1	; oligos_5-8nt_m1 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=1/85; ncol2=16; w=16; offset=1; strand=D; shift=8; score= 3.4; --------wwtGmCACGTGkCaww- ; cor=0.971; Ncor=0.863; logoDP=7.466; NsEucl=0.973; NSW=0.988; rcor=3; rNcor=1; rlogoDP=10; rNsEucl=1; rNSW=2; rank_mean=3.400; match_rank=1 a 0 0 0 0 0 0 0 0 103 108 52 9 150 0 310 3 1 0 2 4 24 183 94 89 0 c 0 0 0 0 0 0 0 0 60 56 55 8 165 317 1 311 5 9 1 1 279 30 62 68 0 g 0 0 0 0 0 0 0 0 68 62 30 279 1 1 9 5 311 1 317 165 8 55 56 60 0 t 0 0 0 0 0 0 0 0 89 94 183 24 4 2 0 1 3 310 0 150 9 52 108 103 0
ABI5.DAP_M0201_AthalianaCistrome_shift6 (ABI5.DAP:M0201:AthalianaCistrome)	0.839	0.751	7.331	0.944	0.947	41	4	12	10	29	19.200	9	; oligos_5-8nt_m1 versus ABI5.DAP_M0201_AthalianaCistrome (ABI5.DAP:M0201:AthalianaCistrome); m=9/85; ncol2=18; w=17; offset=-1; strand=D; shift=6; score= 19.2; ------wdrwgrwsACGTGKCarw- ; cor=0.839; Ncor=0.751; logoDP=7.331; NsEucl=0.944; NSW=0.947; rcor=41; rNcor=4; rlogoDP=12; rNsEucl=10; rNSW=29; rank_mean=19.200; match_rank=9 a 0 0 0 0 0 0 241 217 224 161 44 157 198 0 595 0 0 0 0 0 27 394 151 190 0 c 0 0 0 0 0 0 71 59 80 39 19 119 92 289 0 595 0 0 0 0 568 50 124 117 0 g 0 0 0 0 0 0 131 167 158 98 400 296 0 294 0 0 595 0 595 446 0 123 174 87 0 t 0 0 0 0 0 0 152 152 133 297 132 23 305 12 0 0 0 595 0 149 0 28 146 201 0
PIF3_PIF3_2_Athamap_rc_shift7 (PIF3:PIF3_2:Athamap_rc)	0.870	0.821	2.117	0.948	0.955	25	2	63	8	17	23.000	15	; oligos_5-8nt_m1 versus PIF3_PIF3_2_Athamap_rc (PIF3:PIF3_2:Athamap_rc); m=15/85; ncol2=17; w=17; offset=0; strand=R; shift=7; score= 23; -------rsbkbCCACGTGGbyhy- ; cor=0.870; Ncor=0.821; logoDP=2.117; NsEucl=0.948; NSW=0.955; rcor=25; rNcor=2; rlogoDP=63; rNsEucl=8; rNSW=17; rank_mean=23.000; match_rank=15 a 0 0 0 0 0 0 0 11 6 0 2 2 0 0 32 0 0 0 0 0 0 7 9 6 0 c 0 0 0 0 0 0 0 6 11 8 0 11 32 32 0 32 0 0 0 5 13 13 10 9 0 g 0 0 0 0 0 0 0 11 8 13 15 10 0 0 0 0 32 0 32 26 11 2 4 2 0 t 0 0 0 0 0 0 0 4 7 11 15 9 0 0 0 0 0 32 0 1 8 10 9 15 0
PIF3_PIF3_1_Athamap_shift7 (PIF3:PIF3_1:Athamap)	0.795	0.795	7.516	0.940	0.935	65	3	8	22	43	28.200	22	; oligos_5-8nt_m1 versus PIF3_PIF3_1_Athamap (PIF3:PIF3_1:Athamap); m=22/85; ncol2=18; w=18; offset=0; strand=D; shift=7; score= 28.2; -------gkrggmCACGTGrmswCk ; cor=0.795; Ncor=0.795; logoDP=7.516; NsEucl=0.940; NSW=0.935; rcor=65; rNcor=3; rlogoDP=8; rNsEucl=22; rNSW=43; rank_mean=28.200; match_rank=22 a 0 0 0 0 0 0 0 2 5 11 6 5 11 0 27 0 0 0 0 11 9 3 11 4 4 c 0 0 0 0 0 0 0 5 1 2 0 3 11 27 0 27 0 0 0 2 12 9 6 19 2 g 0 0 0 0 0 0 0 15 10 12 17 17 5 0 0 0 27 0 27 13 6 13 0 4 9 t 0 0 0 0 0 0 0 5 11 2 4 2 0 0 0 0 0 27 0 1 0 2 10 0 12