One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/07/compare-matrices_2019-07-07.122309_UxxYka/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_2019-07-07.122309_UxxYka/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift2 ; 10 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_shift2 (oligos_5-8nt_m1)
; oligos_5-8nt_m1; m=0 (reference); ncol1=21; shift=2; ncol=27; --rwrwrrwTTTGGCGGGAAAah---- ; Alignment reference a 0 0 7 8 11 11 8 11 12 5 1 1 3 0 5 2 1 0 21 21 19 12 8 0 0 0 0 c 0 0 4 4 1 2 3 0 1 1 2 0 1 1 18 0 0 0 1 0 2 3 7 0 0 0 0 g 0 0 8 5 7 5 8 8 4 1 0 3 21 24 1 23 24 25 1 3 3 4 1 0 0 0 0 t 0 0 6 8 6 7 6 6 8 18 22 21 0 0 1 0 0 0 2 1 1 6 9 0 0 0 0

DEL2.DAP_M0363_AthalianaCistrome_shift2 (DEL2.DAP:M0363:AthalianaCistrome) 0.938 0.893 11.367 0.961 0.969 4 1 4 2 2 2.600 1
; oligos_5-8nt_m1 versus DEL2.DAP_M0363_AthalianaCistrome (DEL2.DAP:M0363:AthalianaCistrome); m=1/9; ncol2=20; w=20; offset=0; strand=D; shift=2; score= 2.6; --wwwwdtTTTTGGCGGGAAAA----- ; cor=0.938; Ncor=0.893; logoDP=11.367; NsEucl=0.961; NSW=0.969; rcor=4; rNcor=1; rlogoDP=4; rNsEucl=2; rNSW=2; rank_mean=2.600; match_rank=1 a 0 0 192 234 317 185 180 131 61 38 28 21 7 2 15 5 0 33 570 565 527 399 0 0 0 0 0 c 0 0 25 25 23 138 29 18 11 3 4 0 7 0 550 0 8 6 0 2 15 41 0 0 0 0 0 g 0 0 111 56 65 49 166 103 21 4 12 12 550 574 0 571 566 532 6 7 12 18 0 0 0 0 0 t 0 0 248 261 171 204 201 324 483 531 532 543 12 0 11 0 2 5 0 2 22 118 0 0 0 0 0

DEL1.ampDAP_M0365_AthalianaCistrome_shift7 (DEL1.ampDAP:M0365:AthalianaCistrome) 0.949 0.678 12.496 0.950 0.963 2 4 2 3 4 3.000 2
; oligos_5-8nt_m1 versus DEL1.ampDAP_M0365_AthalianaCistrome (DEL1.ampDAP:M0365:AthalianaCistrome); m=2/9; ncol2=15; w=15; offset=5; strand=D; shift=7; score= 3; -------tTTTTGGCGGGAAAA----- ; cor=0.949; Ncor=0.678; logoDP=12.496; NsEucl=0.950; NSW=0.963; rcor=2; rNcor=4; rlogoDP=2; rNsEucl=3; rNSW=4; rank_mean=3.000; match_rank=2 a 0 0 0 0 0 0 0 136 64 16 9 10 5 2 1 0 0 10 581 584 541 419 0 0 0 0 0 c 0 0 0 0 0 0 0 6 2 0 0 1 4 0 583 0 11 3 0 0 5 33 0 0 0 0 0 g 0 0 0 0 0 0 0 125 12 0 1 3 571 582 0 583 572 569 3 0 9 16 0 0 0 0 0 t 0 0 0 0 0 0 0 317 506 568 574 570 4 0 0 1 1 2 0 0 29 116 0 0 0 0 0

REM16.DAP_M0005_AthalianaCistrome_shift1 (REM16.DAP:M0005:AthalianaCistrome) 0.869 0.790 11.821 0.941 0.930 6 2 3 6 6 4.600 5
; oligos_5-8nt_m1 versus REM16.DAP_M0005_AthalianaCistrome (REM16.DAP:M0005:AthalianaCistrome); m=5/9; ncol2=21; w=20; offset=-1; strand=D; shift=1; score= 4.6; -TTTaykkTTTTGGCGGGAAAA----- ; cor=0.869; Ncor=0.790; logoDP=11.821; NsEucl=0.941; NSW=0.930; rcor=6; rNcor=2; rlogoDP=3; rNsEucl=6; rNSW=6; rank_mean=4.600; match_rank=5 a 0 57 54 33 146 23 26 19 0 0 1 0 5 12 0 6 2 31 241 241 240 219 0 0 0 0 0 c 0 14 4 11 7 128 4 1 1 1 2 2 2 0 236 0 0 1 1 1 0 8 0 0 0 0 0 g 0 5 10 11 33 10 138 75 6 0 0 0 228 229 0 235 240 210 0 0 2 0 0 0 0 0 0 t 0 166 174 187 56 81 74 147 235 241 239 240 7 1 6 1 0 0 0 0 0 15 0 0 0 0 0

ARF16.DAP_M0142_AthalianaCistrome_shift1 (ARF16.DAP:M0142:AthalianaCistrome) 0.776 0.706 9.317 0.925 0.886 7 3 5 7 9 6.200 7
; oligos_5-8nt_m1 versus ARF16.DAP_M0142_AthalianaCistrome (ARF16.DAP:M0142:AthalianaCistrome); m=7/9; ncol2=21; w=20; offset=-1; strand=D; shift=1; score= 6.2; -TTTACGkTTTTGGCGGrAAAA----- ; cor=0.776; Ncor=0.706; logoDP=9.317; NsEucl=0.925; NSW=0.886; rcor=7; rNcor=3; rlogoDP=5; rNsEucl=7; rNSW=9; rank_mean=6.200; match_rank=7 a 0 4 3 3 86 0 7 9 0 1 3 3 2 9 0 6 16 35 95 97 99 90 0 0 0 0 0 c 0 1 0 4 0 87 1 2 0 0 0 2 0 0 92 1 2 0 0 2 0 1 0 0 0 0 0 g 0 1 0 1 12 0 91 40 2 0 1 0 93 92 2 92 81 66 6 2 1 1 0 0 0 0 0 t 0 95 98 93 3 14 2 50 99 100 97 96 6 0 7 2 2 0 0 0 1 9 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_shift2 (oligos_5-8nt_m1)													; oligos_5-8nt_m1; m=0 (reference); ncol1=21; shift=2; ncol=27; --rwrwrrwTTTGGCGGGAAAah---- ; Alignment reference a 0 0 7 8 11 11 8 11 12 5 1 1 3 0 5 2 1 0 21 21 19 12 8 0 0 0 0 c 0 0 4 4 1 2 3 0 1 1 2 0 1 1 18 0 0 0 1 0 2 3 7 0 0 0 0 g 0 0 8 5 7 5 8 8 4 1 0 3 21 24 1 23 24 25 1 3 3 4 1 0 0 0 0 t 0 0 6 8 6 7 6 6 8 18 22 21 0 0 1 0 0 0 2 1 1 6 9 0 0 0 0
DEL2.DAP_M0363_AthalianaCistrome_shift2 (DEL2.DAP:M0363:AthalianaCistrome)	0.938	0.893	11.367	0.961	0.969	4	1	4	2	2	2.600	1	; oligos_5-8nt_m1 versus DEL2.DAP_M0363_AthalianaCistrome (DEL2.DAP:M0363:AthalianaCistrome); m=1/9; ncol2=20; w=20; offset=0; strand=D; shift=2; score= 2.6; --wwwwdtTTTTGGCGGGAAAA----- ; cor=0.938; Ncor=0.893; logoDP=11.367; NsEucl=0.961; NSW=0.969; rcor=4; rNcor=1; rlogoDP=4; rNsEucl=2; rNSW=2; rank_mean=2.600; match_rank=1 a 0 0 192 234 317 185 180 131 61 38 28 21 7 2 15 5 0 33 570 565 527 399 0 0 0 0 0 c 0 0 25 25 23 138 29 18 11 3 4 0 7 0 550 0 8 6 0 2 15 41 0 0 0 0 0 g 0 0 111 56 65 49 166 103 21 4 12 12 550 574 0 571 566 532 6 7 12 18 0 0 0 0 0 t 0 0 248 261 171 204 201 324 483 531 532 543 12 0 11 0 2 5 0 2 22 118 0 0 0 0 0
DEL1.ampDAP_M0365_AthalianaCistrome_shift7 (DEL1.ampDAP:M0365:AthalianaCistrome)	0.949	0.678	12.496	0.950	0.963	2	4	2	3	4	3.000	2	; oligos_5-8nt_m1 versus DEL1.ampDAP_M0365_AthalianaCistrome (DEL1.ampDAP:M0365:AthalianaCistrome); m=2/9; ncol2=15; w=15; offset=5; strand=D; shift=7; score= 3; -------tTTTTGGCGGGAAAA----- ; cor=0.949; Ncor=0.678; logoDP=12.496; NsEucl=0.950; NSW=0.963; rcor=2; rNcor=4; rlogoDP=2; rNsEucl=3; rNSW=4; rank_mean=3.000; match_rank=2 a 0 0 0 0 0 0 0 136 64 16 9 10 5 2 1 0 0 10 581 584 541 419 0 0 0 0 0 c 0 0 0 0 0 0 0 6 2 0 0 1 4 0 583 0 11 3 0 0 5 33 0 0 0 0 0 g 0 0 0 0 0 0 0 125 12 0 1 3 571 582 0 583 572 569 3 0 9 16 0 0 0 0 0 t 0 0 0 0 0 0 0 317 506 568 574 570 4 0 0 1 1 2 0 0 29 116 0 0 0 0 0
REM16.DAP_M0005_AthalianaCistrome_shift1 (REM16.DAP:M0005:AthalianaCistrome)	0.869	0.790	11.821	0.941	0.930	6	2	3	6	6	4.600	5	; oligos_5-8nt_m1 versus REM16.DAP_M0005_AthalianaCistrome (REM16.DAP:M0005:AthalianaCistrome); m=5/9; ncol2=21; w=20; offset=-1; strand=D; shift=1; score= 4.6; -TTTaykkTTTTGGCGGGAAAA----- ; cor=0.869; Ncor=0.790; logoDP=11.821; NsEucl=0.941; NSW=0.930; rcor=6; rNcor=2; rlogoDP=3; rNsEucl=6; rNSW=6; rank_mean=4.600; match_rank=5 a 0 57 54 33 146 23 26 19 0 0 1 0 5 12 0 6 2 31 241 241 240 219 0 0 0 0 0 c 0 14 4 11 7 128 4 1 1 1 2 2 2 0 236 0 0 1 1 1 0 8 0 0 0 0 0 g 0 5 10 11 33 10 138 75 6 0 0 0 228 229 0 235 240 210 0 0 2 0 0 0 0 0 0 t 0 166 174 187 56 81 74 147 235 241 239 240 7 1 6 1 0 0 0 0 0 15 0 0 0 0 0
ARF16.DAP_M0142_AthalianaCistrome_shift1 (ARF16.DAP:M0142:AthalianaCistrome)	0.776	0.706	9.317	0.925	0.886	7	3	5	7	9	6.200	7	; oligos_5-8nt_m1 versus ARF16.DAP_M0142_AthalianaCistrome (ARF16.DAP:M0142:AthalianaCistrome); m=7/9; ncol2=21; w=20; offset=-1; strand=D; shift=1; score= 6.2; -TTTACGkTTTTGGCGGrAAAA----- ; cor=0.776; Ncor=0.706; logoDP=9.317; NsEucl=0.925; NSW=0.886; rcor=7; rNcor=3; rlogoDP=5; rNsEucl=7; rNSW=9; rank_mean=6.200; match_rank=7 a 0 4 3 3 86 0 7 9 0 1 3 3 2 9 0 6 16 35 95 97 99 90 0 0 0 0 0 c 0 1 0 4 0 87 1 2 0 0 0 2 0 0 92 1 2 0 0 2 0 1 0 0 0 0 0 g 0 1 0 1 12 0 91 40 2 0 1 0 93 92 2 92 81 66 6 2 1 1 0 0 0 0 0 t 0 95 98 93 3 14 2 50 99 100 97 96 6 0 7 2 2 0 0 0 1 9 0 0 0 0 0