One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/07/compare-matrices_2019-07-07.144256_yQRm5O/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_2019-07-07.144256_yQRm5O/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m2_shift5 ; 11 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_m2_shift5 (oligos_5-8nt_m2)
; oligos_5-8nt_m2; m=0 (reference); ncol1=16; shift=5; ncol=22; -----raamkgGCGGGAAmba- ; Alignment reference a 0 0 0 0 0 12 21 23 18 3 5 1 2 0 0 2 35 36 11 9 15 0 c 0 0 0 0 0 6 6 7 10 4 9 0 34 0 1 3 4 1 18 10 9 0 g 0 0 0 0 0 17 7 4 4 10 21 38 0 39 39 34 1 3 6 10 8 0 t 0 0 0 0 0 5 6 6 8 23 5 1 4 1 0 1 0 0 5 11 8 0

E2Fc_E2Fc_Athamap_rc_shift7 (E2Fc:E2Fc:Athamap_rc) 0.919 0.632 1.063 0.942 0.963 3 3 7 1 3 3.400 1
; oligos_5-8nt_m2 versus E2Fc_E2Fc_Athamap_rc (E2Fc:E2Fc:Athamap_rc); m=1/10; ncol2=11; w=11; offset=2; strand=R; shift=7; score= 3.4; -------wwkgGCGGGAA---- ; cor=0.919; Ncor=0.632; logoDP=1.063; NsEucl=0.942; NSW=0.963; rcor=3; rNcor=3; rlogoDP=7; rNsEucl=1; rNSW=3; rank_mean=3.400; match_rank=1 a 0 0 0 0 0 0 0 2 2 0 1 0 0 0 0 0 4 4 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 1 0 5 0 1 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 2 3 5 0 5 4 5 0 0 0 0 0 0 t 0 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 1 1 0 0 0 0

DEL2.ampDAP_M0366_AthalianaCistrome_shift5 (DEL2.ampDAP:M0366:AthalianaCistrome) 0.731 0.686 9.547 0.900 0.850 8 1 1 9 10 5.800 5
; oligos_5-8nt_m2 versus DEL2.ampDAP_M0366_AthalianaCistrome (DEL2.ampDAP:M0366:AthalianaCistrome); m=5/10; ncol2=15; w=15; offset=0; strand=D; shift=5; score= 5.8; -----tTTTTGGCGGGAAAA-- ; cor=0.731; Ncor=0.686; logoDP=9.547; NsEucl=0.900; NSW=0.850; rcor=8; rNcor=1; rlogoDP=1; rNsEucl=9; rNSW=10; rank_mean=5.800; match_rank=5 a 0 0 0 0 0 114 57 26 20 8 3 0 1 1 1 0 545 549 526 425 0 0 c 0 0 0 0 0 5 1 2 0 1 2 0 548 0 8 6 0 0 7 28 0 0 g 0 0 0 0 0 135 7 1 4 3 543 549 0 547 540 542 4 0 6 12 0 0 t 0 0 0 0 0 295 484 520 525 537 1 0 0 1 0 1 0 0 10 84 0 0

DEL1.ampDAP_M0365_AthalianaCistrome_shift5 (DEL1.ampDAP:M0365:AthalianaCistrome) 0.730 0.684 9.455 0.900 0.851 9 2 2 8 9 6.000 6
; oligos_5-8nt_m2 versus DEL1.ampDAP_M0365_AthalianaCistrome (DEL1.ampDAP:M0365:AthalianaCistrome); m=6/10; ncol2=15; w=15; offset=0; strand=D; shift=5; score= 6; -----tTTTTGGCGGGAAAA-- ; cor=0.730; Ncor=0.684; logoDP=9.455; NsEucl=0.900; NSW=0.851; rcor=9; rNcor=2; rlogoDP=2; rNsEucl=8; rNSW=9; rank_mean=6.000; match_rank=6 a 0 0 0 0 0 136 64 16 9 10 5 2 1 0 0 10 581 584 541 419 0 0 c 0 0 0 0 0 6 2 0 0 1 4 0 583 0 11 3 0 0 5 33 0 0 g 0 0 0 0 0 125 12 0 1 3 571 582 0 583 572 569 3 0 9 16 0 0 t 0 0 0 0 0 317 506 568 574 570 4 0 0 1 1 2 0 0 29 116 0 0

DEL1.DAP_M0367_AthalianaCistrome_rc_shift6 (DEL1.DAP:M0367:AthalianaCistrome_rc) 0.784 0.534 0.318 0.913 0.887 5 4 10 5 7 6.200 8
; oligos_5-8nt_m2 versus DEL1.DAP_M0367_AthalianaCistrome_rc (DEL1.DAP:M0367:AthalianaCistrome_rc); m=8/10; ncol2=21; w=15; offset=1; strand=R; shift=6; score= 6.2; ------TTTTGGCGGGAAAwwt ; cor=0.784; Ncor=0.534; logoDP=0.318; NsEucl=0.913; NSW=0.887; rcor=5; rNcor=4; rlogoDP=10; rNsEucl=5; rNSW=7; rank_mean=6.200; match_rank=8 a 0 0 0 0 0 0 75 44 25 12 1 0 0 0 0 0 325 324 279 203 87 70 c 0 0 0 0 0 0 0 2 4 0 16 1 326 0 3 3 0 1 10 22 36 44 g 0 0 0 0 0 0 5 1 3 11 308 324 0 326 323 323 0 0 13 15 21 57 t 0 0 0 0 0 0 246 279 294 303 1 1 0 0 0 0 1 1 24 86 182 155

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m2_shift5 (oligos_5-8nt_m2)													; oligos_5-8nt_m2; m=0 (reference); ncol1=16; shift=5; ncol=22; -----raamkgGCGGGAAmba- ; Alignment reference a 0 0 0 0 0 12 21 23 18 3 5 1 2 0 0 2 35 36 11 9 15 0 c 0 0 0 0 0 6 6 7 10 4 9 0 34 0 1 3 4 1 18 10 9 0 g 0 0 0 0 0 17 7 4 4 10 21 38 0 39 39 34 1 3 6 10 8 0 t 0 0 0 0 0 5 6 6 8 23 5 1 4 1 0 1 0 0 5 11 8 0
E2Fc_E2Fc_Athamap_rc_shift7 (E2Fc:E2Fc:Athamap_rc)	0.919	0.632	1.063	0.942	0.963	3	3	7	1	3	3.400	1	; oligos_5-8nt_m2 versus E2Fc_E2Fc_Athamap_rc (E2Fc:E2Fc:Athamap_rc); m=1/10; ncol2=11; w=11; offset=2; strand=R; shift=7; score= 3.4; -------wwkgGCGGGAA---- ; cor=0.919; Ncor=0.632; logoDP=1.063; NsEucl=0.942; NSW=0.963; rcor=3; rNcor=3; rlogoDP=7; rNsEucl=1; rNSW=3; rank_mean=3.400; match_rank=1 a 0 0 0 0 0 0 0 2 2 0 1 0 0 0 0 0 4 4 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 1 0 5 0 1 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 2 3 5 0 5 4 5 0 0 0 0 0 0 t 0 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 1 1 0 0 0 0
DEL2.ampDAP_M0366_AthalianaCistrome_shift5 (DEL2.ampDAP:M0366:AthalianaCistrome)	0.731	0.686	9.547	0.900	0.850	8	1	1	9	10	5.800	5	; oligos_5-8nt_m2 versus DEL2.ampDAP_M0366_AthalianaCistrome (DEL2.ampDAP:M0366:AthalianaCistrome); m=5/10; ncol2=15; w=15; offset=0; strand=D; shift=5; score= 5.8; -----tTTTTGGCGGGAAAA-- ; cor=0.731; Ncor=0.686; logoDP=9.547; NsEucl=0.900; NSW=0.850; rcor=8; rNcor=1; rlogoDP=1; rNsEucl=9; rNSW=10; rank_mean=5.800; match_rank=5 a 0 0 0 0 0 114 57 26 20 8 3 0 1 1 1 0 545 549 526 425 0 0 c 0 0 0 0 0 5 1 2 0 1 2 0 548 0 8 6 0 0 7 28 0 0 g 0 0 0 0 0 135 7 1 4 3 543 549 0 547 540 542 4 0 6 12 0 0 t 0 0 0 0 0 295 484 520 525 537 1 0 0 1 0 1 0 0 10 84 0 0
DEL1.ampDAP_M0365_AthalianaCistrome_shift5 (DEL1.ampDAP:M0365:AthalianaCistrome)	0.730	0.684	9.455	0.900	0.851	9	2	2	8	9	6.000	6	; oligos_5-8nt_m2 versus DEL1.ampDAP_M0365_AthalianaCistrome (DEL1.ampDAP:M0365:AthalianaCistrome); m=6/10; ncol2=15; w=15; offset=0; strand=D; shift=5; score= 6; -----tTTTTGGCGGGAAAA-- ; cor=0.730; Ncor=0.684; logoDP=9.455; NsEucl=0.900; NSW=0.851; rcor=9; rNcor=2; rlogoDP=2; rNsEucl=8; rNSW=9; rank_mean=6.000; match_rank=6 a 0 0 0 0 0 136 64 16 9 10 5 2 1 0 0 10 581 584 541 419 0 0 c 0 0 0 0 0 6 2 0 0 1 4 0 583 0 11 3 0 0 5 33 0 0 g 0 0 0 0 0 125 12 0 1 3 571 582 0 583 572 569 3 0 9 16 0 0 t 0 0 0 0 0 317 506 568 574 570 4 0 0 1 1 2 0 0 29 116 0 0
DEL1.DAP_M0367_AthalianaCistrome_rc_shift6 (DEL1.DAP:M0367:AthalianaCistrome_rc)	0.784	0.534	0.318	0.913	0.887	5	4	10	5	7	6.200	8	; oligos_5-8nt_m2 versus DEL1.DAP_M0367_AthalianaCistrome_rc (DEL1.DAP:M0367:AthalianaCistrome_rc); m=8/10; ncol2=21; w=15; offset=1; strand=R; shift=6; score= 6.2; ------TTTTGGCGGGAAAwwt ; cor=0.784; Ncor=0.534; logoDP=0.318; NsEucl=0.913; NSW=0.887; rcor=5; rNcor=4; rlogoDP=10; rNsEucl=5; rNSW=7; rank_mean=6.200; match_rank=8 a 0 0 0 0 0 0 75 44 25 12 1 0 0 0 0 0 325 324 279 203 87 70 c 0 0 0 0 0 0 0 2 4 0 16 1 326 0 3 3 0 1 10 22 36 44 g 0 0 0 0 0 0 5 1 3 11 308 324 0 326 323 323 0 0 13 15 21 57 t 0 0 0 0 0 0 246 279 294 303 1 1 0 0 0 0 1 1 24 86 182 155