One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/02/compare-matrices_2019-07-02.131606_4xeQnO/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_2019-07-02.131606_4xeQnO/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift3 ; 5 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_shift3 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=3; ncol=30; ---khyCTCTywTcCTCTCTCwCTCtm--- ; Alignment reference a 0 0 0 7 9 8 3 0 3 2 6 17 3 4 3 6 0 1 1 4 2 19 1 1 2 8 11 0 0 0 c 0 0 0 8 12 16 27 5 29 3 9 6 6 21 30 2 34 2 28 6 30 4 29 5 29 5 15 0 0 0 g 0 0 0 9 5 0 2 1 2 2 3 1 2 2 1 0 0 0 3 1 2 2 1 1 2 5 1 0 0 0 t 0 0 0 11 9 11 3 29 1 28 17 11 24 8 1 27 1 32 3 24 1 10 4 28 2 17 8 0 0 0

BPC6_MA1402.1_JASPAR_shift6 (BPC6:MA1402.1:JASPAR) 0.806 0.706 9.365 0.931 0.901 1 2 1 2 2 1.600 1
; dyads_test_vs_ctrl_m1 versus BPC6_MA1402.1_JASPAR (BPC6:MA1402.1:JASPAR); m=1/4; ncol2=21; w=21; offset=3; strand=D; shift=6; score= 1.6; ------CTCTCTCTCTCTCTCTCTCTm--- ; cor=0.806; Ncor=0.706; logoDP=9.365; NsEucl=0.931; NSW=0.901; rcor=1; rNcor=2; rlogoDP=1; rNsEucl=2; rNSW=2; rank_mean=1.600; match_rank=1 a 0 0 0 0 0 0 24 18 13 15 12 6 0 2 1 0 1 2 2 0 12 4 12 8 6 3 50 0 0 0 c 0 0 0 0 0 0 134 19 161 7 142 2 160 6 177 1 168 0 186 1 169 3 168 6 170 2 123 0 0 0 g 0 0 0 0 0 0 2 0 10 5 7 5 3 1 2 0 0 0 0 0 0 0 5 0 0 2 1 0 0 0 t 0 0 0 0 0 0 28 151 4 161 27 175 25 179 8 187 19 186 0 187 7 181 3 174 12 181 14 0 0 0

BPC1_MA1404.1_JASPAR_rc_shift3 (BPC1:MA1404.1:JASPAR_rc) 0.775 0.775 0.821 0.934 0.894 2 1 4 1 3 2.200 2
; dyads_test_vs_ctrl_m1 versus BPC1_MA1404.1_JASPAR_rc (BPC1:MA1404.1:JASPAR_rc); m=2/4; ncol2=24; w=24; offset=0; strand=R; shift=3; score= 2.2; ---TCTCTCTCTCTCTCTCTCTCTCTC--- ; cor=0.775; Ncor=0.775; logoDP=0.821; NsEucl=0.934; NSW=0.894; rcor=2; rNcor=1; rlogoDP=4; rNsEucl=1; rNSW=3; rank_mean=2.200; match_rank=2 a 0 0 0 38 45 35 7 14 7 22 21 0 23 23 18 7 2 11 18 14 18 0 15 20 33 23 18 0 0 0 c 0 0 0 43 427 39 440 35 459 9 467 54 462 56 450 3 508 2 482 44 461 39 448 18 483 29 421 0 0 0 g 0 0 0 22 20 15 19 12 2 0 10 0 0 0 9 11 2 6 0 3 17 0 9 0 15 4 18 0 0 0 t 0 0 0 436 47 450 73 478 71 508 41 485 54 460 62 518 27 520 39 478 43 500 67 501 8 483 82 0 0 0

AT3G46070_MA1381.1_JASPAR_shift13 (AT3G46070:MA1381.1:JASPAR) 0.722 0.404 3.697 0.917 0.905 4 4 2 4 1 3.000 3
; dyads_test_vs_ctrl_m1 versus AT3G46070_MA1381.1_JASPAR (AT3G46070:MA1381.1:JASPAR); m=3/4; ncol2=15; w=14; offset=10; strand=D; shift=13; score= 3; -------------yywhyyTCACTcthh-- ; cor=0.722; Ncor=0.404; logoDP=3.697; NsEucl=0.917; NSW=0.905; rcor=4; rNcor=4; rlogoDP=2; rNsEucl=4; rNSW=1; rank_mean=3.000; match_rank=3 a 0 0 0 0 0 0 0 0 0 0 0 0 0 45 27 78 63 18 48 9 0 200 2 0 14 42 59 63 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 53 91 47 55 79 64 0 202 0 200 0 131 44 78 65 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 14 15 8 16 14 19 0 0 0 0 0 22 10 13 16 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 90 69 69 68 91 71 193 0 2 0 202 35 106 52 58 0 0

BPC5_MA1403.1_JASPAR_rc_shift0 (BPC5:MA1403.1:JASPAR_rc) 0.758 0.606 0.839 0.920 0.846 3 3 3 3 4 3.200 4
; dyads_test_vs_ctrl_m1 versus BPC5_MA1403.1_JASPAR_rc (BPC5:MA1403.1:JASPAR_rc); m=4/4; ncol2=30; w=24; offset=-3; strand=R; shift=0; score= 3.2; CTCTCTCTCTCTCTCTCTCTCTCTCTCTCT ; cor=0.758; Ncor=0.606; logoDP=0.839; NsEucl=0.920; NSW=0.846; rcor=3; rNcor=3; rlogoDP=3; rNsEucl=3; rNSW=4; rank_mean=3.200; match_rank=4 a 3 0 0 4 1 1 1 2 0 0 1 3 0 0 0 0 1 0 0 0 0 1 1 3 2 2 2 0 0 0 c 91 0 98 0 99 3 99 0 101 1 99 1 100 1 100 1 97 0 102 0 100 2 100 0 99 0 98 0 99 7 g 3 2 4 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 t 5 100 0 98 1 98 1 100 0 101 1 98 1 101 2 101 4 102 0 102 1 99 0 99 1 100 2 102 3 95

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m1_shift3 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=3; ncol=30; ---khyCTCTywTcCTCTCTCwCTCtm--- ; Alignment reference a 0 0 0 7 9 8 3 0 3 2 6 17 3 4 3 6 0 1 1 4 2 19 1 1 2 8 11 0 0 0 c 0 0 0 8 12 16 27 5 29 3 9 6 6 21 30 2 34 2 28 6 30 4 29 5 29 5 15 0 0 0 g 0 0 0 9 5 0 2 1 2 2 3 1 2 2 1 0 0 0 3 1 2 2 1 1 2 5 1 0 0 0 t 0 0 0 11 9 11 3 29 1 28 17 11 24 8 1 27 1 32 3 24 1 10 4 28 2 17 8 0 0 0
BPC6_MA1402.1_JASPAR_shift6 (BPC6:MA1402.1:JASPAR)	0.806	0.706	9.365	0.931	0.901	1	2	1	2	2	1.600	1	; dyads_test_vs_ctrl_m1 versus BPC6_MA1402.1_JASPAR (BPC6:MA1402.1:JASPAR); m=1/4; ncol2=21; w=21; offset=3; strand=D; shift=6; score= 1.6; ------CTCTCTCTCTCTCTCTCTCTm--- ; cor=0.806; Ncor=0.706; logoDP=9.365; NsEucl=0.931; NSW=0.901; rcor=1; rNcor=2; rlogoDP=1; rNsEucl=2; rNSW=2; rank_mean=1.600; match_rank=1 a 0 0 0 0 0 0 24 18 13 15 12 6 0 2 1 0 1 2 2 0 12 4 12 8 6 3 50 0 0 0 c 0 0 0 0 0 0 134 19 161 7 142 2 160 6 177 1 168 0 186 1 169 3 168 6 170 2 123 0 0 0 g 0 0 0 0 0 0 2 0 10 5 7 5 3 1 2 0 0 0 0 0 0 0 5 0 0 2 1 0 0 0 t 0 0 0 0 0 0 28 151 4 161 27 175 25 179 8 187 19 186 0 187 7 181 3 174 12 181 14 0 0 0
BPC1_MA1404.1_JASPAR_rc_shift3 (BPC1:MA1404.1:JASPAR_rc)	0.775	0.775	0.821	0.934	0.894	2	1	4	1	3	2.200	2	; dyads_test_vs_ctrl_m1 versus BPC1_MA1404.1_JASPAR_rc (BPC1:MA1404.1:JASPAR_rc); m=2/4; ncol2=24; w=24; offset=0; strand=R; shift=3; score= 2.2; ---TCTCTCTCTCTCTCTCTCTCTCTC--- ; cor=0.775; Ncor=0.775; logoDP=0.821; NsEucl=0.934; NSW=0.894; rcor=2; rNcor=1; rlogoDP=4; rNsEucl=1; rNSW=3; rank_mean=2.200; match_rank=2 a 0 0 0 38 45 35 7 14 7 22 21 0 23 23 18 7 2 11 18 14 18 0 15 20 33 23 18 0 0 0 c 0 0 0 43 427 39 440 35 459 9 467 54 462 56 450 3 508 2 482 44 461 39 448 18 483 29 421 0 0 0 g 0 0 0 22 20 15 19 12 2 0 10 0 0 0 9 11 2 6 0 3 17 0 9 0 15 4 18 0 0 0 t 0 0 0 436 47 450 73 478 71 508 41 485 54 460 62 518 27 520 39 478 43 500 67 501 8 483 82 0 0 0
AT3G46070_MA1381.1_JASPAR_shift13 (AT3G46070:MA1381.1:JASPAR)	0.722	0.404	3.697	0.917	0.905	4	4	2	4	1	3.000	3	; dyads_test_vs_ctrl_m1 versus AT3G46070_MA1381.1_JASPAR (AT3G46070:MA1381.1:JASPAR); m=3/4; ncol2=15; w=14; offset=10; strand=D; shift=13; score= 3; -------------yywhyyTCACTcthh-- ; cor=0.722; Ncor=0.404; logoDP=3.697; NsEucl=0.917; NSW=0.905; rcor=4; rNcor=4; rlogoDP=2; rNsEucl=4; rNSW=1; rank_mean=3.000; match_rank=3 a 0 0 0 0 0 0 0 0 0 0 0 0 0 45 27 78 63 18 48 9 0 200 2 0 14 42 59 63 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 53 91 47 55 79 64 0 202 0 200 0 131 44 78 65 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 14 15 8 16 14 19 0 0 0 0 0 22 10 13 16 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 90 69 69 68 91 71 193 0 2 0 202 35 106 52 58 0 0
BPC5_MA1403.1_JASPAR_rc_shift0 (BPC5:MA1403.1:JASPAR_rc)	0.758	0.606	0.839	0.920	0.846	3	3	3	3	4	3.200	4	; dyads_test_vs_ctrl_m1 versus BPC5_MA1403.1_JASPAR_rc (BPC5:MA1403.1:JASPAR_rc); m=4/4; ncol2=30; w=24; offset=-3; strand=R; shift=0; score= 3.2; CTCTCTCTCTCTCTCTCTCTCTCTCTCTCT ; cor=0.758; Ncor=0.606; logoDP=0.839; NsEucl=0.920; NSW=0.846; rcor=3; rNcor=3; rlogoDP=3; rNsEucl=3; rNSW=4; rank_mean=3.200; match_rank=4 a 3 0 0 4 1 1 1 2 0 0 1 3 0 0 0 0 1 0 0 0 0 1 1 3 2 2 2 0 0 0 c 91 0 98 0 99 3 99 0 101 1 99 1 100 1 100 1 97 0 102 0 100 2 100 0 99 0 98 0 99 7 g 3 2 4 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 t 5 100 0 98 1 98 1 100 0 101 1 98 1 101 2 101 4 102 0 102 1 99 0 99 1 100 2 102 3 95