One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.134651_4ba2PC/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_2019-07-04.134651_4ba2PC/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m3_shift6 ; 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

dyads_test_vs_ctrl_m3_shift6 (dyads_test_vs_ctrl_m3)
; dyads_test_vs_ctrl_m3; m=0 (reference); ncol1=21; shift=6; ncol=30; ------mccyaAAACCCwAAmcCCchm--- ; Alignment reference a 0 0 0 0 0 0 47 39 17 25 106 162 165 143 19 4 18 68 132 154 98 41 15 14 32 52 60 0 0 0 c 0 0 0 0 0 0 68 70 112 55 24 7 5 21 146 165 138 28 10 14 67 120 144 130 91 48 48 0 0 0 g 0 0 0 0 0 0 20 26 21 14 12 2 2 5 5 3 4 3 5 8 7 4 5 12 13 21 27 0 0 0 t 0 0 0 0 0 0 43 43 28 84 36 7 6 9 8 6 18 79 31 2 6 13 14 22 42 57 43 0 0 0

TRP2.ampDAP_M0612_AthalianaCistrome_shift4 (TRP2.ampDAP:M0612:AthalianaCistrome) 0.839 0.693 8.596 0.933 0.916 3 2 1 4 4 2.800 1
; dyads_test_vs_ctrl_m3 versus TRP2.ampDAP_M0612_AthalianaCistrome (TRP2.ampDAP:M0612:AthalianaCistrome); m=1/11; ncol2=21; w=19; offset=-2; strand=D; shift=4; score= 2.8; ----AAACCCTAAACCCTAAACCCT----- ; cor=0.839; Ncor=0.693; logoDP=8.596; NsEucl=0.933; NSW=0.916; rcor=3; rNcor=2; rlogoDP=1; 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) 0.839 0.656 8.416 0.928 0.907 2 4 3 5 6 4.000 3
; dyads_test_vs_ctrl_m3 versus TRP2_MA1356.1_JASPAR (TRP2:MA1356.1:JASPAR); m=3/11; ncol2=20; w=18; offset=-2; strand=D; shift=4; score= 4; ----AAACCCTAAACCCTAAACCC------ ; cor=0.839; Ncor=0.656; logoDP=8.416; NsEucl=0.928; NSW=0.907; rcor=2; rNcor=4; rlogoDP=3; rNsEucl=5; rNSW=6; rank_mean=4.000; match_rank=3 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) 0.765 0.698 8.417 0.921 0.868 6 1 2 8 9 5.200 5
; dyads_test_vs_ctrl_m3 versus TRP1_MA1352.1_JASPAR (TRP1:MA1352.1:JASPAR); m=5/11; ncol2=23; w=21; offset=-2; strand=D; shift=4; score= 5.2; ----AAACCCTAAACCCTAAACCCTAA--- ; cor=0.765; Ncor=0.698; logoDP=8.417; NsEucl=0.921; NSW=0.868; rcor=6; rNcor=1; rlogoDP=2; rNsEucl=8; rNSW=9; rank_mean=5.200; 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) 0.726 0.663 6.559 0.919 0.863 10 3 8 10 11 8.400 10
; dyads_test_vs_ctrl_m3 versus SRS7.DAP_M0745_AthalianaCistrome (SRS7.DAP:M0745:AthalianaCistrome); m=10/11; ncol2=23; w=21; offset=-2; strand=D; shift=4; score= 8.4; ----AAACCCTAAACCCTAAACCCTAA--- ; cor=0.726; Ncor=0.663; logoDP=6.559; NsEucl=0.919; NSW=0.863; rcor=10; rNcor=3; rlogoDP=8; rNsEucl=10; rNSW=11; rank_mean=8.400; match_rank=10 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
dyads_test_vs_ctrl_m3_shift6 (dyads_test_vs_ctrl_m3)													; dyads_test_vs_ctrl_m3; m=0 (reference); ncol1=21; shift=6; ncol=30; ------mccyaAAACCCwAAmcCCchm--- ; Alignment reference a 0 0 0 0 0 0 47 39 17 25 106 162 165 143 19 4 18 68 132 154 98 41 15 14 32 52 60 0 0 0 c 0 0 0 0 0 0 68 70 112 55 24 7 5 21 146 165 138 28 10 14 67 120 144 130 91 48 48 0 0 0 g 0 0 0 0 0 0 20 26 21 14 12 2 2 5 5 3 4 3 5 8 7 4 5 12 13 21 27 0 0 0 t 0 0 0 0 0 0 43 43 28 84 36 7 6 9 8 6 18 79 31 2 6 13 14 22 42 57 43 0 0 0
TRP2.ampDAP_M0612_AthalianaCistrome_shift4 (TRP2.ampDAP:M0612:AthalianaCistrome)	0.839	0.693	8.596	0.933	0.916	3	2	1	4	4	2.800	1	; dyads_test_vs_ctrl_m3 versus TRP2.ampDAP_M0612_AthalianaCistrome (TRP2.ampDAP:M0612:AthalianaCistrome); m=1/11; ncol2=21; w=19; offset=-2; strand=D; shift=4; score= 2.8; ----AAACCCTAAACCCTAAACCCT----- ; cor=0.839; Ncor=0.693; logoDP=8.596; NsEucl=0.933; NSW=0.916; rcor=3; rNcor=2; rlogoDP=1; 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)	0.839	0.656	8.416	0.928	0.907	2	4	3	5	6	4.000	3	; dyads_test_vs_ctrl_m3 versus TRP2_MA1356.1_JASPAR (TRP2:MA1356.1:JASPAR); m=3/11; ncol2=20; w=18; offset=-2; strand=D; shift=4; score= 4; ----AAACCCTAAACCCTAAACCC------ ; cor=0.839; Ncor=0.656; logoDP=8.416; NsEucl=0.928; NSW=0.907; rcor=2; rNcor=4; rlogoDP=3; rNsEucl=5; rNSW=6; rank_mean=4.000; match_rank=3 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)	0.765	0.698	8.417	0.921	0.868	6	1	2	8	9	5.200	5	; dyads_test_vs_ctrl_m3 versus TRP1_MA1352.1_JASPAR (TRP1:MA1352.1:JASPAR); m=5/11; ncol2=23; w=21; offset=-2; strand=D; shift=4; score= 5.2; ----AAACCCTAAACCCTAAACCCTAA--- ; cor=0.765; Ncor=0.698; logoDP=8.417; NsEucl=0.921; NSW=0.868; rcor=6; rNcor=1; rlogoDP=2; rNsEucl=8; rNSW=9; rank_mean=5.200; 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)	0.726	0.663	6.559	0.919	0.863	10	3	8	10	11	8.400	10	; dyads_test_vs_ctrl_m3 versus SRS7.DAP_M0745_AthalianaCistrome (SRS7.DAP:M0745:AthalianaCistrome); m=10/11; ncol2=23; w=21; offset=-2; strand=D; shift=4; score= 8.4; ----AAACCCTAAACCCTAAACCCTAA--- ; cor=0.726; Ncor=0.663; logoDP=6.559; NsEucl=0.919; NSW=0.863; rcor=10; rNcor=3; rlogoDP=8; rNsEucl=10; rNSW=11; rank_mean=8.400; match_rank=10 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