One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/07/compare-matrices_2019-07-07.152203_trVUT2/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_2019-07-07.152203_trVUT2/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift6 ; 15 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_shift6 (oligos_5-8nt_m1)
; oligos_5-8nt_m1; m=0 (reference); ncol1=16; shift=6; ncol=22; ------wwTTTCCCGCCAAAwh ; Alignment reference a 0 0 0 0 0 0 7 7 0 3 0 2 0 0 0 0 2 22 19 16 7 8 c 0 0 0 0 0 0 5 3 3 1 0 21 20 20 0 23 17 0 1 2 5 8 g 0 0 0 0 0 0 5 2 1 0 2 0 2 0 21 0 1 0 0 1 2 0 t 0 0 0 0 0 0 6 11 19 19 21 0 1 3 2 0 3 1 3 4 9 7

DEL1.DAP_M0367_AthalianaCistrome_shift0 (DEL1.DAP:M0367:AthalianaCistrome) 0.967 0.660 12.132 0.961 0.977 3 4 1 1 3 2.400 1
; oligos_5-8nt_m1 versus DEL1.DAP_M0367_AthalianaCistrome (DEL1.DAP:M0367:AthalianaCistrome); m=1/14; ncol2=21; w=15; offset=-6; strand=D; shift=0; score= 2.4; amwawawwTTTCCCGCCAAAA- ; cor=0.967; Ncor=0.660; logoDP=12.132; NsEucl=0.961; NSW=0.977; rcor=3; rNcor=4; rlogoDP=1; rNsEucl=1; rNSW=3; rank_mean=2.400; match_rank=1 a 138 150 132 143 144 155 182 86 24 1 1 0 0 0 0 1 1 303 294 279 246 0 c 72 102 78 59 43 57 21 15 13 0 0 323 323 326 0 324 308 11 3 1 5 0 g 46 21 17 65 29 44 36 22 10 1 0 3 3 0 326 1 16 0 4 2 0 0 t 70 53 99 59 110 70 87 203 279 324 325 0 0 0 0 0 1 12 25 44 75 0

DEL1.ampDAP_M0365_AthalianaCistrome_rc_shift7 (DEL1.ampDAP:M0365:AthalianaCistrome_rc) 0.957 0.897 4.324 0.953 0.967 5 1 8 4 6 4.800 4
; oligos_5-8nt_m1 versus DEL1.ampDAP_M0365_AthalianaCistrome_rc (DEL1.ampDAP:M0365:AthalianaCistrome_rc); m=4/14; ncol2=15; w=15; offset=1; strand=R; shift=7; score= 4.8; -------TTTTCCCGCCAAAAa ; cor=0.957; Ncor=0.897; logoDP=4.324; NsEucl=0.953; NSW=0.967; rcor=5; rNcor=1; rlogoDP=8; rNsEucl=4; rNSW=6; rank_mean=4.800; match_rank=4 a 0 0 0 0 0 0 0 116 29 0 0 2 1 1 0 0 4 570 574 568 506 317 c 0 0 0 0 0 0 0 16 9 0 3 569 572 583 0 582 571 3 1 0 12 125 g 0 0 0 0 0 0 0 33 5 0 0 3 11 0 583 0 4 1 0 0 2 6 t 0 0 0 0 0 0 0 419 541 584 581 10 0 0 1 2 5 10 9 16 64 136

DEL2.DAP_M0363_AthalianaCistrome_rc_shift7 (DEL2.DAP:M0363:AthalianaCistrome_rc) 0.957 0.684 0.647 0.957 0.972 4 3 14 2 4 5.400 5
; oligos_5-8nt_m1 versus DEL2.DAP_M0363_AthalianaCistrome_rc (DEL2.DAP:M0363:AthalianaCistrome_rc); m=5/14; ncol2=20; w=15; offset=1; strand=R; shift=7; score= 5.4; -------TTTTCCCGCCAAAAa ; cor=0.957; Ncor=0.684; logoDP=0.647; NsEucl=0.957; NSW=0.972; rcor=4; rNcor=3; rlogoDP=14; rNsEucl=2; rNSW=4; rank_mean=5.400; match_rank=5 a 0 0 0 0 0 0 0 118 22 2 0 5 2 0 11 0 12 543 532 531 483 324 c 0 0 0 0 0 0 0 18 12 7 6 532 566 571 0 574 550 12 12 4 21 103 g 0 0 0 0 0 0 0 41 15 2 0 6 8 0 550 0 7 0 4 3 11 18 t 0 0 0 0 0 0 0 399 527 565 570 33 0 5 15 2 7 21 28 38 61 131

DEL2.ampDAP_M0366_AthalianaCistrome_rc_shift7 (DEL2.ampDAP:M0366:AthalianaCistrome_rc) 0.956 0.896 4.123 0.952 0.966 6 2 9 5 7 5.800 7
; oligos_5-8nt_m1 versus DEL2.ampDAP_M0366_AthalianaCistrome_rc (DEL2.ampDAP:M0366:AthalianaCistrome_rc); m=7/14; ncol2=15; w=15; offset=1; strand=R; shift=7; score= 5.8; -------TTTTCCCGCCAAAAa ; cor=0.956; Ncor=0.896; logoDP=4.123; NsEucl=0.952; NSW=0.966; rcor=6; rNcor=2; rlogoDP=9; rNsEucl=5; rNSW=7; rank_mean=5.800; match_rank=7 a 0 0 0 0 0 0 0 84 10 0 0 1 0 1 0 0 1 537 525 520 484 295 c 0 0 0 0 0 0 0 12 6 0 4 542 540 547 0 549 543 3 4 1 7 135 g 0 0 0 0 0 0 0 28 7 0 0 6 8 0 548 0 2 1 0 2 1 5 t 0 0 0 0 0 0 0 425 526 549 545 0 1 1 1 0 3 8 20 26 57 114

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m1_shift6 (oligos_5-8nt_m1)													; oligos_5-8nt_m1; m=0 (reference); ncol1=16; shift=6; ncol=22; ------wwTTTCCCGCCAAAwh ; Alignment reference a 0 0 0 0 0 0 7 7 0 3 0 2 0 0 0 0 2 22 19 16 7 8 c 0 0 0 0 0 0 5 3 3 1 0 21 20 20 0 23 17 0 1 2 5 8 g 0 0 0 0 0 0 5 2 1 0 2 0 2 0 21 0 1 0 0 1 2 0 t 0 0 0 0 0 0 6 11 19 19 21 0 1 3 2 0 3 1 3 4 9 7
DEL1.DAP_M0367_AthalianaCistrome_shift0 (DEL1.DAP:M0367:AthalianaCistrome)	0.967	0.660	12.132	0.961	0.977	3	4	1	1	3	2.400	1	; oligos_5-8nt_m1 versus DEL1.DAP_M0367_AthalianaCistrome (DEL1.DAP:M0367:AthalianaCistrome); m=1/14; ncol2=21; w=15; offset=-6; strand=D; shift=0; score= 2.4; amwawawwTTTCCCGCCAAAA- ; cor=0.967; Ncor=0.660; logoDP=12.132; NsEucl=0.961; NSW=0.977; rcor=3; rNcor=4; rlogoDP=1; rNsEucl=1; rNSW=3; rank_mean=2.400; match_rank=1 a 138 150 132 143 144 155 182 86 24 1 1 0 0 0 0 1 1 303 294 279 246 0 c 72 102 78 59 43 57 21 15 13 0 0 323 323 326 0 324 308 11 3 1 5 0 g 46 21 17 65 29 44 36 22 10 1 0 3 3 0 326 1 16 0 4 2 0 0 t 70 53 99 59 110 70 87 203 279 324 325 0 0 0 0 0 1 12 25 44 75 0
DEL1.ampDAP_M0365_AthalianaCistrome_rc_shift7 (DEL1.ampDAP:M0365:AthalianaCistrome_rc)	0.957	0.897	4.324	0.953	0.967	5	1	8	4	6	4.800	4	; oligos_5-8nt_m1 versus DEL1.ampDAP_M0365_AthalianaCistrome_rc (DEL1.ampDAP:M0365:AthalianaCistrome_rc); m=4/14; ncol2=15; w=15; offset=1; strand=R; shift=7; score= 4.8; -------TTTTCCCGCCAAAAa ; cor=0.957; Ncor=0.897; logoDP=4.324; NsEucl=0.953; NSW=0.967; rcor=5; rNcor=1; rlogoDP=8; rNsEucl=4; rNSW=6; rank_mean=4.800; match_rank=4 a 0 0 0 0 0 0 0 116 29 0 0 2 1 1 0 0 4 570 574 568 506 317 c 0 0 0 0 0 0 0 16 9 0 3 569 572 583 0 582 571 3 1 0 12 125 g 0 0 0 0 0 0 0 33 5 0 0 3 11 0 583 0 4 1 0 0 2 6 t 0 0 0 0 0 0 0 419 541 584 581 10 0 0 1 2 5 10 9 16 64 136
DEL2.DAP_M0363_AthalianaCistrome_rc_shift7 (DEL2.DAP:M0363:AthalianaCistrome_rc)	0.957	0.684	0.647	0.957	0.972	4	3	14	2	4	5.400	5	; oligos_5-8nt_m1 versus DEL2.DAP_M0363_AthalianaCistrome_rc (DEL2.DAP:M0363:AthalianaCistrome_rc); m=5/14; ncol2=20; w=15; offset=1; strand=R; shift=7; score= 5.4; -------TTTTCCCGCCAAAAa ; cor=0.957; Ncor=0.684; logoDP=0.647; NsEucl=0.957; NSW=0.972; rcor=4; rNcor=3; rlogoDP=14; rNsEucl=2; rNSW=4; rank_mean=5.400; match_rank=5 a 0 0 0 0 0 0 0 118 22 2 0 5 2 0 11 0 12 543 532 531 483 324 c 0 0 0 0 0 0 0 18 12 7 6 532 566 571 0 574 550 12 12 4 21 103 g 0 0 0 0 0 0 0 41 15 2 0 6 8 0 550 0 7 0 4 3 11 18 t 0 0 0 0 0 0 0 399 527 565 570 33 0 5 15 2 7 21 28 38 61 131
DEL2.ampDAP_M0366_AthalianaCistrome_rc_shift7 (DEL2.ampDAP:M0366:AthalianaCistrome_rc)	0.956	0.896	4.123	0.952	0.966	6	2	9	5	7	5.800	7	; oligos_5-8nt_m1 versus DEL2.ampDAP_M0366_AthalianaCistrome_rc (DEL2.ampDAP:M0366:AthalianaCistrome_rc); m=7/14; ncol2=15; w=15; offset=1; strand=R; shift=7; score= 5.8; -------TTTTCCCGCCAAAAa ; cor=0.956; Ncor=0.896; logoDP=4.123; NsEucl=0.952; NSW=0.966; rcor=6; rNcor=2; rlogoDP=9; rNsEucl=5; rNSW=7; rank_mean=5.800; match_rank=7 a 0 0 0 0 0 0 0 84 10 0 0 1 0 1 0 0 1 537 525 520 484 295 c 0 0 0 0 0 0 0 12 6 0 4 542 540 547 0 549 543 3 4 1 7 135 g 0 0 0 0 0 0 0 28 7 0 0 6 8 0 548 0 2 1 0 2 1 5 t 0 0 0 0 0 0 0 425 526 549 545 0 1 1 1 0 3 8 20 26 57 114