One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/02/compare-matrices_2019-07-02.112058_WI8i8i/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/2019/07/02/compare-matrices_2019-07-02.112058_WI8i8i/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift0 ; 7 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_m1_shift0 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; wwgtGGCCCAAAww ; Alignment reference a 344 277 193 171 69 58 79 52 62 991 895 813 389 279 c 217 215 102 93 20 16 872 960 953 39 73 95 228 254 g 215 232 572 89 958 972 70 21 32 20 44 76 156 220 t 317 369 226 740 46 47 72 60 46 43 81 109 320 340

LOC_Os02g42380_M1657_1.02_CISBP_shift1 (LOC_Os02g42380:M1657_1.02:CISBP) 0.706 0.504 3.479 0.896 0.892 2 3 4 1 1 2.200 1
; dyads_test_vs_ctrl_m1 versus LOC_Os02g42380_M1657_1.02_CISBP (LOC_Os02g42380:M1657_1.02:CISBP); m=1/6; ncol2=10; w=10; offset=1; strand=D; shift=1; score= 2.2; -kkGGgcCCmm--- ; cor=0.706; Ncor=0.504; logoDP=3.479; NsEucl=0.896; NSW=0.892; rcor=2; rNcor=3; rlogoDP=4; rNsEucl=1; rNSW=1; rank_mean=2.200; match_rank=1 a 0 18 7 0 0.0000 13 11 0.0000 7 45 28 0 0 0 c 0 13 15 0 0.0000 10 66 1.0000 93 33 41 0 0 0 g 0 41 33 93 1.0000 66 10 0.0000 0 15 13 0 0 0 t 0 28 45 7 0.0000 11 13 0.0000 0 7 18 0 0 0

TCP23_TCP23_ArabidopsisPBM_shift2 (TCP23:TCP23:ArabidopsisPBM) 0.729 0.521 5.457 0.880 0.855 1 2 1 4 4 2.400 2
; dyads_test_vs_ctrl_m1 versus TCP23_TCP23_ArabidopsisPBM (TCP23:TCP23:ArabidopsisPBM); m=2/6; ncol2=10; w=10; offset=2; strand=D; shift=2; score= 2.4; --GGGGCCCACA-- ; cor=0.729; Ncor=0.521; logoDP=5.457; NsEucl=0.880; NSW=0.855; rcor=1; rNcor=2; rlogoDP=1; rNsEucl=4; rNSW=4; rank_mean=2.400; match_rank=2 a 0 0 2 0 1 3 1 0 1 96 1 74 0 0 c 0 0 5 0 1 9 97 98 98 1 96 14 0 0 g 0 0 77 97 98 84 1 2 0 3 1 2 0 0 t 0 0 16 3 0 4 1 0 1 0 2 10 0 0

OJ1581_MA1031.1_JASPAR_shift1 (OJ1581:MA1031.1:JASPAR) 0.705 0.504 3.474 0.896 0.891 3 4 5 2 2 3.200 3
; dyads_test_vs_ctrl_m1 versus OJ1581_MA1031.1_JASPAR (OJ1581:MA1031.1:JASPAR); m=3/6; ncol2=10; w=10; offset=1; strand=D; shift=1; score= 3.2; -kkGGgcCCmm--- ; cor=0.705; Ncor=0.504; logoDP=3.474; NsEucl=0.896; NSW=0.891; rcor=3; rNcor=4; rlogoDP=5; rNsEucl=2; rNSW=2; rank_mean=3.200; match_rank=3 a 0 175 74 0 0 127 112 0 71 445 279 0 0 0 c 0 131 146 0 0 101 661 1000 929 335 414 0 0 0 g 0 414 335 929 1000 661 101 0 0 146 131 0 0 0 t 0 279 445 71 0 112 127 0 0 74 175 0 0 0

TCP16.ampDAP_M0753_AthalianaCistrome_rc_shift0 (TCP16.ampDAP:M0753:AthalianaCistrome_rc) 0.700 0.550 2.022 0.895 0.878 6 1 6 3 3 3.800 4
; dyads_test_vs_ctrl_m1 versus TCP16.ampDAP_M0753_AthalianaCistrome_rc (TCP16.ampDAP:M0753:AthalianaCistrome_rc); m=4/6; ncol2=11; w=11; offset=0; strand=R; shift=0; score= 3.8; wkGTGGaCCyr--- ; cor=0.700; Ncor=0.550; logoDP=2.022; NsEucl=0.895; NSW=0.878; rcor=6; rNcor=1; rlogoDP=6; rNsEucl=3; rNSW=3; rank_mean=3.800; match_rank=4 a 160 89 11 0 2 0 307 3 0 38 240 0 0 0 c 92 24 1 4 2 0 39 546 545 321 69 0 0 0 g 88 242 539 0 547 551 82 2 0 9 161 0 0 0 t 211 196 0 547 0 0 123 0 6 183 81 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_m1_shift0 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; wwgtGGCCCAAAww ; Alignment reference a 344 277 193 171 69 58 79 52 62 991 895 813 389 279 c 217 215 102 93 20 16 872 960 953 39 73 95 228 254 g 215 232 572 89 958 972 70 21 32 20 44 76 156 220 t 317 369 226 740 46 47 72 60 46 43 81 109 320 340
LOC_Os02g42380_M1657_1.02_CISBP_shift1 (LOC_Os02g42380:M1657_1.02:CISBP)	0.706	0.504	3.479	0.896	0.892	2	3	4	1	1	2.200	1	; dyads_test_vs_ctrl_m1 versus LOC_Os02g42380_M1657_1.02_CISBP (LOC_Os02g42380:M1657_1.02:CISBP); m=1/6; ncol2=10; w=10; offset=1; strand=D; shift=1; score= 2.2; -kkGGgcCCmm--- ; cor=0.706; Ncor=0.504; logoDP=3.479; NsEucl=0.896; NSW=0.892; rcor=2; rNcor=3; rlogoDP=4; rNsEucl=1; rNSW=1; rank_mean=2.200; match_rank=1 a 0 18 7 0 0.0000 13 11 0.0000 7 45 28 0 0 0 c 0 13 15 0 0.0000 10 66 1.0000 93 33 41 0 0 0 g 0 41 33 93 1.0000 66 10 0.0000 0 15 13 0 0 0 t 0 28 45 7 0.0000 11 13 0.0000 0 7 18 0 0 0
TCP23_TCP23_ArabidopsisPBM_shift2 (TCP23:TCP23:ArabidopsisPBM)	0.729	0.521	5.457	0.880	0.855	1	2	1	4	4	2.400	2	; dyads_test_vs_ctrl_m1 versus TCP23_TCP23_ArabidopsisPBM (TCP23:TCP23:ArabidopsisPBM); m=2/6; ncol2=10; w=10; offset=2; strand=D; shift=2; score= 2.4; --GGGGCCCACA-- ; cor=0.729; Ncor=0.521; logoDP=5.457; NsEucl=0.880; NSW=0.855; rcor=1; rNcor=2; rlogoDP=1; rNsEucl=4; rNSW=4; rank_mean=2.400; match_rank=2 a 0 0 2 0 1 3 1 0 1 96 1 74 0 0 c 0 0 5 0 1 9 97 98 98 1 96 14 0 0 g 0 0 77 97 98 84 1 2 0 3 1 2 0 0 t 0 0 16 3 0 4 1 0 1 0 2 10 0 0
OJ1581_MA1031.1_JASPAR_shift1 (OJ1581:MA1031.1:JASPAR)	0.705	0.504	3.474	0.896	0.891	3	4	5	2	2	3.200	3	; dyads_test_vs_ctrl_m1 versus OJ1581_MA1031.1_JASPAR (OJ1581:MA1031.1:JASPAR); m=3/6; ncol2=10; w=10; offset=1; strand=D; shift=1; score= 3.2; -kkGGgcCCmm--- ; cor=0.705; Ncor=0.504; logoDP=3.474; NsEucl=0.896; NSW=0.891; rcor=3; rNcor=4; rlogoDP=5; rNsEucl=2; rNSW=2; rank_mean=3.200; match_rank=3 a 0 175 74 0 0 127 112 0 71 445 279 0 0 0 c 0 131 146 0 0 101 661 1000 929 335 414 0 0 0 g 0 414 335 929 1000 661 101 0 0 146 131 0 0 0 t 0 279 445 71 0 112 127 0 0 74 175 0 0 0
TCP16.ampDAP_M0753_AthalianaCistrome_rc_shift0 (TCP16.ampDAP:M0753:AthalianaCistrome_rc)	0.700	0.550	2.022	0.895	0.878	6	1	6	3	3	3.800	4	; dyads_test_vs_ctrl_m1 versus TCP16.ampDAP_M0753_AthalianaCistrome_rc (TCP16.ampDAP:M0753:AthalianaCistrome_rc); m=4/6; ncol2=11; w=11; offset=0; strand=R; shift=0; score= 3.8; wkGTGGaCCyr--- ; cor=0.700; Ncor=0.550; logoDP=2.022; NsEucl=0.895; NSW=0.878; rcor=6; rNcor=1; rlogoDP=6; rNsEucl=3; rNSW=3; rank_mean=3.800; match_rank=4 a 160 89 11 0 2 0 307 3 0 38 240 0 0 0 c 92 24 1 4 2 0 39 546 545 321 69 0 0 0 g 88 242 539 0 547 551 82 2 0 9 161 0 0 0 t 211 196 0 547 0 0 123 0 6 183 81 0 0 0