One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.133826_tPY5jc/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/2019/07/04/compare-matrices_2019-07-04.133826_tPY5jc/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m2_shift3 ; 12 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_shift3 (oligos_5-8nt_m2)
; oligos_5-8nt_m2; m=0 (reference); ncol1=24; shift=3; ncol=30; ---mmaasCymAAACCCtAAAmCCCwm--- ; Alignment reference a 0 0 0 32 33 43 46 22 10 11 33 86 86 85 7 2 0 12 81 84 75 53 8 6 8 28 28 0 0 0 c 0 0 0 34 35 23 21 24 67 52 36 4 5 5 81 84 92 20 5 6 15 26 79 77 68 21 32 0 0 0 g 0 0 0 10 12 9 12 38 7 7 4 6 2 2 2 3 2 1 1 4 3 2 3 6 3 7 13 0 0 0 t 0 0 0 20 16 21 17 12 12 26 23 0 3 4 6 7 2 63 9 2 3 15 6 7 17 40 23 0 0 0

TRP2.ampDAP_M0612_AthalianaCistrome_shift4 (TRP2.ampDAP:M0612:AthalianaCistrome) 0.837 0.732 10.272 0.937 0.918 3 1 2 4 4 2.800 1
; oligos_5-8nt_m2 versus TRP2.ampDAP_M0612_AthalianaCistrome (TRP2.ampDAP:M0612:AthalianaCistrome); m=1/11; ncol2=21; w=21; offset=1; strand=D; shift=4; score= 2.8; ----AAACCCTAAACCCTAAACCCT----- ; cor=0.837; Ncor=0.732; logoDP=10.272; NsEucl=0.937; NSW=0.918; rcor=3; rNcor=1; rlogoDP=2; rNsEucl=4; rNSW=4; rank_mean=2.800; match_rank=1 a 0 0 0 0 90 85 87 0 9 7 12 103 104 101 2 1 0 5 99 99 97 7 14 4 11 0 0 0 0 0 c 0 0 0 0 3 2 1 85 88 75 2 0 0 3 102 103 102 0 0 0 0 80 75 76 10 0 0 0 0 0 g 0 0 0 0 2 4 1 5 5 5 1 1 0 0 0 0 0 0 4 3 2 1 1 1 5 0 0 0 0 0 t 0 0 0 0 9 13 15 14 2 17 89 0 0 0 0 0 2 99 1 2 5 16 14 23 78 0 0 0 0 0

TRP2_MA1356.1_JASPAR_shift4 (TRP2:MA1356.1:JASPAR) 0.845 0.704 9.957 0.933 0.910 2 3 3 5 6 3.800 2
; oligos_5-8nt_m2 versus TRP2_MA1356.1_JASPAR (TRP2:MA1356.1:JASPAR); m=2/11; ncol2=20; w=20; offset=1; strand=D; shift=4; score= 3.8; ----AAACCCTAAACCCTAAACCC------ ; cor=0.845; Ncor=0.704; logoDP=9.957; NsEucl=0.933; NSW=0.910; rcor=2; rNcor=3; rlogoDP=3; rNsEucl=5; rNSW=6; rank_mean=3.800; match_rank=2 a 0 0 0 0 72 72 72 0 6 0 3 72 76 75 0 2 2 2 73 68 73 1 7 7 0 0 0 0 0 0 c 0 0 0 0 0 0 0 66 63 65 1 0 0 0 75 74 71 0 0 6 0 69 62 61 0 0 0 0 0 0 g 0 0 0 0 1 2 0 2 2 1 1 0 0 0 1 0 3 3 1 0 2 0 2 2 0 0 0 0 0 0 t 0 0 0 0 3 2 4 8 5 10 71 4 0 1 0 0 0 71 2 2 1 6 5 6 0 0 0 0 0 0

TRP1_MA1352.1_JASPAR_shift4 (TRP1:MA1352.1:JASPAR) 0.761 0.729 10.414 0.924 0.868 6 2 1 7 8 4.800 5
; oligos_5-8nt_m2 versus TRP1_MA1352.1_JASPAR (TRP1:MA1352.1:JASPAR); m=5/11; ncol2=23; w=23; offset=1; strand=D; shift=4; score= 4.8; ----AAACCCTAAACCCTAAACCCTAA--- ; cor=0.761; Ncor=0.729; logoDP=10.414; NsEucl=0.924; NSW=0.868; rcor=6; rNcor=2; rlogoDP=1; rNsEucl=7; rNSW=8; rank_mean=4.800; match_rank=5 a 0 0 0 0 45 44 47 0 5 2 0 47 47 48 0 4 0 1 47 43 46 0 8 3 2 47 44 0 0 0 c 0 0 0 0 0 0 0 44 39 36 0 0 0 0 43 43 47 0 0 2 0 43 39 45 1 0 0 0 0 0 g 0 0 0 0 0 0 0 1 2 5 0 0 1 0 0 0 1 0 0 0 2 1 0 0 0 0 0 0 0 0 t 0 0 0 0 3 4 1 3 2 5 48 1 0 0 5 1 0 47 1 3 0 4 1 0 45 1 4 0 0 0

SRS7.DAP_M0745_AthalianaCistrome_shift4 (SRS7.DAP:M0745:AthalianaCistrome) 0.735 0.704 8.260 0.924 0.866 8 4 6 9 9 7.200 7
; oligos_5-8nt_m2 versus SRS7.DAP_M0745_AthalianaCistrome (SRS7.DAP:M0745:AthalianaCistrome); m=7/11; ncol2=23; w=23; offset=1; strand=D; shift=4; score= 7.2; ----AAACCCTAAACCCTAAACCCTAA--- ; cor=0.735; Ncor=0.704; logoDP=8.260; NsEucl=0.924; NSW=0.866; rcor=8; rNcor=4; rlogoDP=6; rNsEucl=9; rNSW=9; rank_mean=7.200; match_rank=7 a 0 0 0 0 24 22 25 0 0 2 0 23 21 22 1 2 0 0 24 17 23 2 0 0 2 25 22 0 0 0 c 0 0 0 0 0 0 0 22 24 23 0 0 0 0 22 21 21 0 0 0 1 21 22 23 0 0 0 0 0 0 g 0 0 0 0 0 1 0 1 1 0 0 0 1 1 1 0 1 0 0 4 0 0 0 0 0 0 2 0 0 0 t 0 0 0 0 1 2 0 2 0 0 25 2 3 2 1 2 3 25 1 4 1 2 3 2 23 0 1 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m2_shift3 (oligos_5-8nt_m2)													; oligos_5-8nt_m2; m=0 (reference); ncol1=24; shift=3; ncol=30; ---mmaasCymAAACCCtAAAmCCCwm--- ; Alignment reference a 0 0 0 32 33 43 46 22 10 11 33 86 86 85 7 2 0 12 81 84 75 53 8 6 8 28 28 0 0 0 c 0 0 0 34 35 23 21 24 67 52 36 4 5 5 81 84 92 20 5 6 15 26 79 77 68 21 32 0 0 0 g 0 0 0 10 12 9 12 38 7 7 4 6 2 2 2 3 2 1 1 4 3 2 3 6 3 7 13 0 0 0 t 0 0 0 20 16 21 17 12 12 26 23 0 3 4 6 7 2 63 9 2 3 15 6 7 17 40 23 0 0 0
TRP2.ampDAP_M0612_AthalianaCistrome_shift4 (TRP2.ampDAP:M0612:AthalianaCistrome)	0.837	0.732	10.272	0.937	0.918	3	1	2	4	4	2.800	1	; oligos_5-8nt_m2 versus TRP2.ampDAP_M0612_AthalianaCistrome (TRP2.ampDAP:M0612:AthalianaCistrome); m=1/11; ncol2=21; w=21; offset=1; strand=D; shift=4; score= 2.8; ----AAACCCTAAACCCTAAACCCT----- ; cor=0.837; Ncor=0.732; logoDP=10.272; NsEucl=0.937; NSW=0.918; rcor=3; rNcor=1; rlogoDP=2; rNsEucl=4; rNSW=4; rank_mean=2.800; match_rank=1 a 0 0 0 0 90 85 87 0 9 7 12 103 104 101 2 1 0 5 99 99 97 7 14 4 11 0 0 0 0 0 c 0 0 0 0 3 2 1 85 88 75 2 0 0 3 102 103 102 0 0 0 0 80 75 76 10 0 0 0 0 0 g 0 0 0 0 2 4 1 5 5 5 1 1 0 0 0 0 0 0 4 3 2 1 1 1 5 0 0 0 0 0 t 0 0 0 0 9 13 15 14 2 17 89 0 0 0 0 0 2 99 1 2 5 16 14 23 78 0 0 0 0 0
TRP2_MA1356.1_JASPAR_shift4 (TRP2:MA1356.1:JASPAR)	0.845	0.704	9.957	0.933	0.910	2	3	3	5	6	3.800	2	; oligos_5-8nt_m2 versus TRP2_MA1356.1_JASPAR (TRP2:MA1356.1:JASPAR); m=2/11; ncol2=20; w=20; offset=1; strand=D; shift=4; score= 3.8; ----AAACCCTAAACCCTAAACCC------ ; cor=0.845; Ncor=0.704; logoDP=9.957; NsEucl=0.933; NSW=0.910; rcor=2; rNcor=3; rlogoDP=3; rNsEucl=5; rNSW=6; rank_mean=3.800; match_rank=2 a 0 0 0 0 72 72 72 0 6 0 3 72 76 75 0 2 2 2 73 68 73 1 7 7 0 0 0 0 0 0 c 0 0 0 0 0 0 0 66 63 65 1 0 0 0 75 74 71 0 0 6 0 69 62 61 0 0 0 0 0 0 g 0 0 0 0 1 2 0 2 2 1 1 0 0 0 1 0 3 3 1 0 2 0 2 2 0 0 0 0 0 0 t 0 0 0 0 3 2 4 8 5 10 71 4 0 1 0 0 0 71 2 2 1 6 5 6 0 0 0 0 0 0
TRP1_MA1352.1_JASPAR_shift4 (TRP1:MA1352.1:JASPAR)	0.761	0.729	10.414	0.924	0.868	6	2	1	7	8	4.800	5	; oligos_5-8nt_m2 versus TRP1_MA1352.1_JASPAR (TRP1:MA1352.1:JASPAR); m=5/11; ncol2=23; w=23; offset=1; strand=D; shift=4; score= 4.8; ----AAACCCTAAACCCTAAACCCTAA--- ; cor=0.761; Ncor=0.729; logoDP=10.414; NsEucl=0.924; NSW=0.868; rcor=6; rNcor=2; rlogoDP=1; rNsEucl=7; rNSW=8; rank_mean=4.800; match_rank=5 a 0 0 0 0 45 44 47 0 5 2 0 47 47 48 0 4 0 1 47 43 46 0 8 3 2 47 44 0 0 0 c 0 0 0 0 0 0 0 44 39 36 0 0 0 0 43 43 47 0 0 2 0 43 39 45 1 0 0 0 0 0 g 0 0 0 0 0 0 0 1 2 5 0 0 1 0 0 0 1 0 0 0 2 1 0 0 0 0 0 0 0 0 t 0 0 0 0 3 4 1 3 2 5 48 1 0 0 5 1 0 47 1 3 0 4 1 0 45 1 4 0 0 0
SRS7.DAP_M0745_AthalianaCistrome_shift4 (SRS7.DAP:M0745:AthalianaCistrome)	0.735	0.704	8.260	0.924	0.866	8	4	6	9	9	7.200	7	; oligos_5-8nt_m2 versus SRS7.DAP_M0745_AthalianaCistrome (SRS7.DAP:M0745:AthalianaCistrome); m=7/11; ncol2=23; w=23; offset=1; strand=D; shift=4; score= 7.2; ----AAACCCTAAACCCTAAACCCTAA--- ; cor=0.735; Ncor=0.704; logoDP=8.260; NsEucl=0.924; NSW=0.866; rcor=8; rNcor=4; rlogoDP=6; rNsEucl=9; rNSW=9; rank_mean=7.200; match_rank=7 a 0 0 0 0 24 22 25 0 0 2 0 23 21 22 1 2 0 0 24 17 23 2 0 0 2 25 22 0 0 0 c 0 0 0 0 0 0 0 22 24 23 0 0 0 0 22 21 21 0 0 0 1 21 22 23 0 0 0 0 0 0 g 0 0 0 0 0 1 0 1 1 0 0 0 1 1 1 0 1 0 0 4 0 0 0 0 0 0 2 0 0 0 t 0 0 0 0 1 2 0 2 0 0 25 2 3 2 1 2 3 25 1 4 1 2 3 2 23 0 1 0 0 0