One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/apache/2019/10/25/compare-matrices_2019-10-25.161848_Hs70tQ/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/apache/2019/10/25/compare-matrices_2019-10-25.161848_Hs70tQ/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift0 ; 8 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_shift0 (oligos_5-8nt_m1)
; oligos_5-8nt_m1; m=0 (reference); ncol1=23; shift=0; ncol=29; rwccrwdrwtTTGGCGGGAAArw------ ; Alignment reference a 10 7 5 4 6 9 6 10 10 5 3 3 1 0 1 4 0 1 19 19 19 10 7 0 0 0 0 0 0 c 2 3 8 9 4 2 2 0 3 1 0 0 0 0 18 0 0 0 1 0 0 1 5 0 0 0 0 0 0 g 7 5 4 4 8 5 8 9 2 2 2 2 20 22 0 18 22 21 0 2 2 6 4 0 0 0 0 0 0 t 3 7 5 5 4 6 6 3 7 14 17 17 1 0 3 0 0 0 2 1 1 5 6 0 0 0 0 0 0

DEL2.DAP_M0363_AthalianaCistrome_shift2 (DEL2.DAP:M0363:AthalianaCistrome) 0.901 0.783 11.739 0.953 0.955 5 1 4 2 5 3.400 3
; oligos_5-8nt_m1 versus DEL2.DAP_M0363_AthalianaCistrome (DEL2.DAP:M0363:AthalianaCistrome); m=3/7; ncol2=20; w=20; offset=2; strand=D; shift=2; score= 3.4; --wwwwdtTTTTGGCGGGAAAA------- ; cor=0.901; Ncor=0.783; logoDP=11.739; NsEucl=0.953; NSW=0.955; rcor=5; rNcor=1; rlogoDP=4; rNsEucl=2; rNSW=5; rank_mean=3.400; match_rank=3 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 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 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 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 0 0

DEL2.ampDAP_M0366_AthalianaCistrome_shift7 (DEL2.ampDAP:M0366:AthalianaCistrome) 0.935 0.610 13.004 0.945 0.955 3 5 1 5 4 3.600 4
; oligos_5-8nt_m1 versus DEL2.ampDAP_M0366_AthalianaCistrome (DEL2.ampDAP:M0366:AthalianaCistrome); m=4/7; ncol2=15; w=15; offset=7; strand=D; shift=7; score= 3.6; -------tTTTTGGCGGGAAAA------- ; cor=0.935; Ncor=0.610; logoDP=13.004; NsEucl=0.945; NSW=0.955; rcor=3; rNcor=5; rlogoDP=1; rNsEucl=5; rNSW=4; rank_mean=3.600; match_rank=4 a 0 0 0 0 0 0 0 114 57 26 20 8 3 0 1 1 1 0 545 549 526 425 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 5 1 2 0 1 2 0 548 0 8 6 0 0 7 28 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 135 7 1 4 3 543 549 0 547 540 542 4 0 6 12 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 295 484 520 525 537 1 0 0 1 0 1 0 0 10 84 0 0 0 0 0 0 0

REM16.DAP_M0005_AthalianaCistrome_shift1 (REM16.DAP:M0005:AthalianaCistrome) 0.836 0.763 12.192 0.937 0.917 6 2 3 6 6 4.600 6
; oligos_5-8nt_m1 versus REM16.DAP_M0005_AthalianaCistrome (REM16.DAP:M0005:AthalianaCistrome); m=6/7; ncol2=21; w=21; offset=1; strand=D; shift=1; score= 4.6; -TTTaykkTTTTGGCGGGAAAA------- ; cor=0.836; Ncor=0.763; logoDP=12.192; NsEucl=0.937; NSW=0.917; rcor=6; rNcor=2; rlogoDP=3; rNsEucl=6; rNSW=6; rank_mean=4.600; match_rank=6 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 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 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 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 0 0

ARF16.DAP_M0142_AthalianaCistrome_shift1 (ARF16.DAP:M0142:AthalianaCistrome) 0.738 0.674 9.598 0.921 0.869 7 3 5 7 7 5.800 7
; oligos_5-8nt_m1 versus ARF16.DAP_M0142_AthalianaCistrome (ARF16.DAP:M0142:AthalianaCistrome); m=7/7; ncol2=21; w=21; offset=1; strand=D; shift=1; score= 5.8; -TTTACGkTTTTGGCGGrAAAA------- ; cor=0.738; Ncor=0.674; logoDP=9.598; NsEucl=0.921; NSW=0.869; rcor=7; rNcor=3; rlogoDP=5; rNsEucl=7; rNSW=7; rank_mean=5.800; 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 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 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 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 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m1_shift0 (oligos_5-8nt_m1)													; oligos_5-8nt_m1; m=0 (reference); ncol1=23; shift=0; ncol=29; rwccrwdrwtTTGGCGGGAAArw------ ; Alignment reference a 10 7 5 4 6 9 6 10 10 5 3 3 1 0 1 4 0 1 19 19 19 10 7 0 0 0 0 0 0 c 2 3 8 9 4 2 2 0 3 1 0 0 0 0 18 0 0 0 1 0 0 1 5 0 0 0 0 0 0 g 7 5 4 4 8 5 8 9 2 2 2 2 20 22 0 18 22 21 0 2 2 6 4 0 0 0 0 0 0 t 3 7 5 5 4 6 6 3 7 14 17 17 1 0 3 0 0 0 2 1 1 5 6 0 0 0 0 0 0
DEL2.DAP_M0363_AthalianaCistrome_shift2 (DEL2.DAP:M0363:AthalianaCistrome)	0.901	0.783	11.739	0.953	0.955	5	1	4	2	5	3.400	3	; oligos_5-8nt_m1 versus DEL2.DAP_M0363_AthalianaCistrome (DEL2.DAP:M0363:AthalianaCistrome); m=3/7; ncol2=20; w=20; offset=2; strand=D; shift=2; score= 3.4; --wwwwdtTTTTGGCGGGAAAA------- ; cor=0.901; Ncor=0.783; logoDP=11.739; NsEucl=0.953; NSW=0.955; rcor=5; rNcor=1; rlogoDP=4; rNsEucl=2; rNSW=5; rank_mean=3.400; match_rank=3 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 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 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 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 0 0
DEL2.ampDAP_M0366_AthalianaCistrome_shift7 (DEL2.ampDAP:M0366:AthalianaCistrome)	0.935	0.610	13.004	0.945	0.955	3	5	1	5	4	3.600	4	; oligos_5-8nt_m1 versus DEL2.ampDAP_M0366_AthalianaCistrome (DEL2.ampDAP:M0366:AthalianaCistrome); m=4/7; ncol2=15; w=15; offset=7; strand=D; shift=7; score= 3.6; -------tTTTTGGCGGGAAAA------- ; cor=0.935; Ncor=0.610; logoDP=13.004; NsEucl=0.945; NSW=0.955; rcor=3; rNcor=5; rlogoDP=1; rNsEucl=5; rNSW=4; rank_mean=3.600; match_rank=4 a 0 0 0 0 0 0 0 114 57 26 20 8 3 0 1 1 1 0 545 549 526 425 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 5 1 2 0 1 2 0 548 0 8 6 0 0 7 28 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 135 7 1 4 3 543 549 0 547 540 542 4 0 6 12 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 295 484 520 525 537 1 0 0 1 0 1 0 0 10 84 0 0 0 0 0 0 0
REM16.DAP_M0005_AthalianaCistrome_shift1 (REM16.DAP:M0005:AthalianaCistrome)	0.836	0.763	12.192	0.937	0.917	6	2	3	6	6	4.600	6	; oligos_5-8nt_m1 versus REM16.DAP_M0005_AthalianaCistrome (REM16.DAP:M0005:AthalianaCistrome); m=6/7; ncol2=21; w=21; offset=1; strand=D; shift=1; score= 4.6; -TTTaykkTTTTGGCGGGAAAA------- ; cor=0.836; Ncor=0.763; logoDP=12.192; NsEucl=0.937; NSW=0.917; rcor=6; rNcor=2; rlogoDP=3; rNsEucl=6; rNSW=6; rank_mean=4.600; match_rank=6 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 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 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 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 0 0
ARF16.DAP_M0142_AthalianaCistrome_shift1 (ARF16.DAP:M0142:AthalianaCistrome)	0.738	0.674	9.598	0.921	0.869	7	3	5	7	7	5.800	7	; oligos_5-8nt_m1 versus ARF16.DAP_M0142_AthalianaCistrome (ARF16.DAP:M0142:AthalianaCistrome); m=7/7; ncol2=21; w=21; offset=1; strand=D; shift=1; score= 5.8; -TTTACGkTTTTGGCGGrAAAA------- ; cor=0.738; Ncor=0.674; logoDP=9.598; NsEucl=0.921; NSW=0.869; rcor=7; rNcor=3; rlogoDP=5; rNsEucl=7; rNSW=7; rank_mean=5.800; 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 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 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 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 0 0