One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/07/compare-matrices_2019-07-07.120743_sDktAC/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/2019/07/07/compare-matrices_2019-07-07.120743_sDktAC/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m3_shift7 ; 105 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_shift7 (oligos_5-8nt_m3)
; oligos_5-8nt_m3; m=0 (reference); ncol1=18; shift=7; ncol=25; -------wrtgGACACGTGkCagaa ; Alignment reference a 0 0 0 0 0 0 0 60 60 43 28 21 136 6 179 5 10 6 10 14 20 99 41 62 68 c 0 0 0 0 0 0 0 34 33 41 40 8 38 168 0 173 3 4 4 12 142 24 29 46 39 g 0 0 0 0 0 0 0 41 50 38 80 144 9 4 6 3 166 1 170 115 13 37 90 37 40 t 0 0 0 0 0 0 0 55 47 68 42 17 7 12 5 9 11 179 6 49 15 30 30 45 43

HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR) 0.940 0.836 7.644 0.963 0.978 9 1 10 3 8 6.200 1
; oligos_5-8nt_m3 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=1/104; ncol2=16; w=16; offset=1; strand=D; shift=8; score= 6.2; --------wwtGmCACGTGkCaww- ; cor=0.940; Ncor=0.836; logoDP=7.644; NsEucl=0.963; NSW=0.978; rcor=9; rNcor=1; rlogoDP=10; rNsEucl=3; rNSW=8; rank_mean=6.200; 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

AREB3.ampDAP_M0218_AthalianaCistrome_shift7 (AREB3.ampDAP:M0218:AthalianaCistrome) 0.929 0.774 7.652 0.956 0.972 11 4 9 9 11 8.800 2
; oligos_5-8nt_m3 versus AREB3.ampDAP_M0218_AthalianaCistrome (AREB3.ampDAP:M0218:AthalianaCistrome); m=2/104; ncol2=15; w=15; offset=0; strand=D; shift=7; score= 8.8; -------dwwggwsACGTGKCA--- ; cor=0.929; Ncor=0.774; logoDP=7.652; NsEucl=0.956; NSW=0.972; rcor=11; rNcor=4; rlogoDP=9; rNsEucl=9; rNSW=11; rank_mean=8.800; match_rank=2 a 0 0 0 0 0 0 0 229 234 193 71 130 272 0 593 0 0 0 0 0 3 474 0 0 0 c 0 0 0 0 0 0 0 48 53 44 42 79 83 356 0 592 0 0 0 0 590 39 0 0 0 g 0 0 0 0 0 0 0 156 137 88 337 352 0 227 0 1 593 0 593 425 0 57 0 0 0 t 0 0 0 0 0 0 0 160 169 268 143 32 238 10 0 0 0 593 0 168 0 23 0 0 0

ABI5.DAP_M0201_AthalianaCistrome_shift6 (ABI5.DAP:M0201:AthalianaCistrome) 0.886 0.793 7.458 0.953 0.962 37 3 19 13 25 19.400 7
; oligos_5-8nt_m3 versus ABI5.DAP_M0201_AthalianaCistrome (ABI5.DAP:M0201:AthalianaCistrome); m=7/104; ncol2=18; w=17; offset=-1; strand=D; shift=6; score= 19.4; ------wdrwgrwsACGTGKCarw- ; cor=0.886; Ncor=0.793; logoDP=7.458; NsEucl=0.953; NSW=0.962; rcor=37; rNcor=3; rlogoDP=19; rNsEucl=13; rNSW=25; rank_mean=19.400; match_rank=7 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_1_Athamap_shift7 (PIF3:PIF3_1:Athamap) 0.808 0.808 7.857 0.942 0.939 76 2 6 31 49 32.800 24
; oligos_5-8nt_m3 versus PIF3_PIF3_1_Athamap (PIF3:PIF3_1:Athamap); m=24/104; ncol2=18; w=18; offset=0; strand=D; shift=7; score= 32.8; -------gkrggmCACGTGrmswCk ; cor=0.808; Ncor=0.808; logoDP=7.857; NsEucl=0.942; NSW=0.939; rcor=76; rNcor=2; rlogoDP=6; rNsEucl=31; rNSW=49; rank_mean=32.800; match_rank=24 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_m3_shift7 (oligos_5-8nt_m3)													; oligos_5-8nt_m3; m=0 (reference); ncol1=18; shift=7; ncol=25; -------wrtgGACACGTGkCagaa ; Alignment reference a 0 0 0 0 0 0 0 60 60 43 28 21 136 6 179 5 10 6 10 14 20 99 41 62 68 c 0 0 0 0 0 0 0 34 33 41 40 8 38 168 0 173 3 4 4 12 142 24 29 46 39 g 0 0 0 0 0 0 0 41 50 38 80 144 9 4 6 3 166 1 170 115 13 37 90 37 40 t 0 0 0 0 0 0 0 55 47 68 42 17 7 12 5 9 11 179 6 49 15 30 30 45 43
HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR)	0.940	0.836	7.644	0.963	0.978	9	1	10	3	8	6.200	1	; oligos_5-8nt_m3 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=1/104; ncol2=16; w=16; offset=1; strand=D; shift=8; score= 6.2; --------wwtGmCACGTGkCaww- ; cor=0.940; Ncor=0.836; logoDP=7.644; NsEucl=0.963; NSW=0.978; rcor=9; rNcor=1; rlogoDP=10; rNsEucl=3; rNSW=8; rank_mean=6.200; 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
AREB3.ampDAP_M0218_AthalianaCistrome_shift7 (AREB3.ampDAP:M0218:AthalianaCistrome)	0.929	0.774	7.652	0.956	0.972	11	4	9	9	11	8.800	2	; oligos_5-8nt_m3 versus AREB3.ampDAP_M0218_AthalianaCistrome (AREB3.ampDAP:M0218:AthalianaCistrome); m=2/104; ncol2=15; w=15; offset=0; strand=D; shift=7; score= 8.8; -------dwwggwsACGTGKCA--- ; cor=0.929; Ncor=0.774; logoDP=7.652; NsEucl=0.956; NSW=0.972; rcor=11; rNcor=4; rlogoDP=9; rNsEucl=9; rNSW=11; rank_mean=8.800; match_rank=2 a 0 0 0 0 0 0 0 229 234 193 71 130 272 0 593 0 0 0 0 0 3 474 0 0 0 c 0 0 0 0 0 0 0 48 53 44 42 79 83 356 0 592 0 0 0 0 590 39 0 0 0 g 0 0 0 0 0 0 0 156 137 88 337 352 0 227 0 1 593 0 593 425 0 57 0 0 0 t 0 0 0 0 0 0 0 160 169 268 143 32 238 10 0 0 0 593 0 168 0 23 0 0 0
ABI5.DAP_M0201_AthalianaCistrome_shift6 (ABI5.DAP:M0201:AthalianaCistrome)	0.886	0.793	7.458	0.953	0.962	37	3	19	13	25	19.400	7	; oligos_5-8nt_m3 versus ABI5.DAP_M0201_AthalianaCistrome (ABI5.DAP:M0201:AthalianaCistrome); m=7/104; ncol2=18; w=17; offset=-1; strand=D; shift=6; score= 19.4; ------wdrwgrwsACGTGKCarw- ; cor=0.886; Ncor=0.793; logoDP=7.458; NsEucl=0.953; NSW=0.962; rcor=37; rNcor=3; rlogoDP=19; rNsEucl=13; rNSW=25; rank_mean=19.400; match_rank=7 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_1_Athamap_shift7 (PIF3:PIF3_1:Athamap)	0.808	0.808	7.857	0.942	0.939	76	2	6	31	49	32.800	24	; oligos_5-8nt_m3 versus PIF3_PIF3_1_Athamap (PIF3:PIF3_1:Athamap); m=24/104; ncol2=18; w=18; offset=0; strand=D; shift=7; score= 32.8; -------gkrggmCACGTGrmswCk ; cor=0.808; Ncor=0.808; logoDP=7.857; NsEucl=0.942; NSW=0.939; rcor=76; rNcor=2; rlogoDP=6; rNsEucl=31; rNSW=49; rank_mean=32.800; match_rank=24 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