One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/07/compare-matrices_2019-07-07.132351_dFLNG5/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_2019-07-07.132351_dFLNG5/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift1 ; 29 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_shift1 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=1; ncol=18; -kwCGGkahwCCGAvs-- ; Alignment reference a 0 4 8 1 1 0 4 9 6 8 0 0 2 18 7 2 0 0 c 0 4 4 22 0 0 4 5 6 5 21 23 1 2 10 8 0 0 g 0 6 2 1 23 24 7 5 3 4 2 0 20 2 6 11 0 0 t 0 10 10 0 0 0 9 5 9 7 1 1 1 2 1 3 0 0

DEAR3_DEAR3_2_ArabidopsisPBM_shift6 (DEAR3:DEAR3_2:ArabidopsisPBM) 0.820 0.547 3.258 0.918 0.933 6 1 6 6 7 5.200 1
; dyads_test_vs_ctrl_m1 versus DEAR3_DEAR3_2_ArabidopsisPBM (DEAR3:DEAR3_2:ArabidopsisPBM); m=1/28; ncol2=10; w=10; offset=5; strand=D; shift=6; score= 5.2; ------bgaACCGACs-- ; cor=0.820; Ncor=0.547; logoDP=3.258; NsEucl=0.918; NSW=0.933; rcor=6; rNcor=1; rlogoDP=6; rNsEucl=6; rNSW=7; rank_mean=5.200; match_rank=1 a 0 0 0 0 0 0 11 12 59 88 2 2 3 82 2 16 0 0 c 0 0 0 0 0 0 33 16 9 2 96 96 2 8 96 32 0 0 g 0 0 0 0 0 0 28 60 11 9 1 1 94 6 0 39 0 0 t 0 0 0 0 0 0 28 12 21 1 1 1 1 4 2 13 0 0

HRD_M0019_1.02_CISBP_shift7 (HRD:M0019_1.02:CISBP) 0.831 0.499 2.271 0.931 0.957 3 2 24 1 1 6.200 3
; dyads_test_vs_ctrl_m1 versus HRD_M0019_1.02_CISBP (HRD:M0019_1.02:CISBP); m=3/28; ncol2=9; w=9; offset=6; strand=D; shift=7; score= 6.2; -------ytrCCGaCa-- ; cor=0.831; Ncor=0.499; logoDP=2.271; NsEucl=0.931; NSW=0.957; rcor=3; rNcor=2; rlogoDP=24; rNsEucl=1; rNSW=1; rank_mean=6.200; match_rank=3 a 0 0 0 0 0 0 0 19 17 31 0 4 4 53 9 42 0 0 c 0 0 0 0 0 0 0 29 23 4 89 88 4 24 71 16 0 0 g 0 0 0 0 0 0 0 23 19 58 2 4 90 8 10 22 0 0 t 0 0 0 0 0 0 0 29 41 7 9 4 2 15 10 20 0 0

AT1G75490_M0015_1.02_CISBP_shift7 (AT1G75490:M0015_1.02:CISBP) 0.804 0.483 2.456 0.928 0.953 9 3 21 2 2 7.400 4
; dyads_test_vs_ctrl_m1 versus AT1G75490_M0015_1.02_CISBP (AT1G75490:M0015_1.02:CISBP); m=4/28; ncol2=9; w=9; offset=6; strand=D; shift=7; score= 7.4; -------scrCCGmyw-- ; cor=0.804; Ncor=0.483; logoDP=2.456; NsEucl=0.928; NSW=0.953; rcor=9; rNcor=3; rlogoDP=21; rNsEucl=2; rNSW=2; rank_mean=7.400; match_rank=4 a 0 0 0 0 0 0 0 21 22 61 2 3 6 35 22 32 0 0 c 0 0 0 0 0 0 0 28 42 0 95 91 0 31 38 24 0 0 g 0 0 0 0 0 0 0 27 18 39 3 2 86 12 15 16 0 0 t 0 0 0 0 0 0 0 24 18 0 0 4 8 22 25 28 0 0

ERF039_MA0995.1_JASPAR_rc_shift7 (ERF039:MA0995.1:JASPAR_rc) 0.838 0.471 2.438 0.923 0.946 2 5 22 4 5 7.600 6
; dyads_test_vs_ctrl_m1 versus ERF039_MA0995.1_JASPAR_rc (ERF039:MA0995.1:JASPAR_rc); m=6/28; ncol2=10; w=9; offset=6; strand=R; shift=7; score= 7.6; -------ycrCCGaCay- ; cor=0.838; Ncor=0.471; logoDP=2.438; NsEucl=0.923; NSW=0.946; rcor=2; rNcor=5; rlogoDP=22; rNsEucl=4; rNSW=5; rank_mean=7.600; match_rank=6 a 0 0 0 0 0 0 0 198 190 524 7 12 5 660 34 473 240 0 c 0 0 0 0 0 0 0 316 395 39 965 980 2 140 912 120 274 0 g 0 0 0 0 0 0 0 225 170 416 8 2 989 86 11 242 236 0 t 0 0 0 0 0 0 0 261 244 20 19 6 4 115 43 165 250 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m1_shift1 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=1; ncol=18; -kwCGGkahwCCGAvs-- ; Alignment reference a 0 4 8 1 1 0 4 9 6 8 0 0 2 18 7 2 0 0 c 0 4 4 22 0 0 4 5 6 5 21 23 1 2 10 8 0 0 g 0 6 2 1 23 24 7 5 3 4 2 0 20 2 6 11 0 0 t 0 10 10 0 0 0 9 5 9 7 1 1 1 2 1 3 0 0
DEAR3_DEAR3_2_ArabidopsisPBM_shift6 (DEAR3:DEAR3_2:ArabidopsisPBM)	0.820	0.547	3.258	0.918	0.933	6	1	6	6	7	5.200	1	; dyads_test_vs_ctrl_m1 versus DEAR3_DEAR3_2_ArabidopsisPBM (DEAR3:DEAR3_2:ArabidopsisPBM); m=1/28; ncol2=10; w=10; offset=5; strand=D; shift=6; score= 5.2; ------bgaACCGACs-- ; cor=0.820; Ncor=0.547; logoDP=3.258; NsEucl=0.918; NSW=0.933; rcor=6; rNcor=1; rlogoDP=6; rNsEucl=6; rNSW=7; rank_mean=5.200; match_rank=1 a 0 0 0 0 0 0 11 12 59 88 2 2 3 82 2 16 0 0 c 0 0 0 0 0 0 33 16 9 2 96 96 2 8 96 32 0 0 g 0 0 0 0 0 0 28 60 11 9 1 1 94 6 0 39 0 0 t 0 0 0 0 0 0 28 12 21 1 1 1 1 4 2 13 0 0
HRD_M0019_1.02_CISBP_shift7 (HRD:M0019_1.02:CISBP)	0.831	0.499	2.271	0.931	0.957	3	2	24	1	1	6.200	3	; dyads_test_vs_ctrl_m1 versus HRD_M0019_1.02_CISBP (HRD:M0019_1.02:CISBP); m=3/28; ncol2=9; w=9; offset=6; strand=D; shift=7; score= 6.2; -------ytrCCGaCa-- ; cor=0.831; Ncor=0.499; logoDP=2.271; NsEucl=0.931; NSW=0.957; rcor=3; rNcor=2; rlogoDP=24; rNsEucl=1; rNSW=1; rank_mean=6.200; match_rank=3 a 0 0 0 0 0 0 0 19 17 31 0 4 4 53 9 42 0 0 c 0 0 0 0 0 0 0 29 23 4 89 88 4 24 71 16 0 0 g 0 0 0 0 0 0 0 23 19 58 2 4 90 8 10 22 0 0 t 0 0 0 0 0 0 0 29 41 7 9 4 2 15 10 20 0 0
AT1G75490_M0015_1.02_CISBP_shift7 (AT1G75490:M0015_1.02:CISBP)	0.804	0.483	2.456	0.928	0.953	9	3	21	2	2	7.400	4	; dyads_test_vs_ctrl_m1 versus AT1G75490_M0015_1.02_CISBP (AT1G75490:M0015_1.02:CISBP); m=4/28; ncol2=9; w=9; offset=6; strand=D; shift=7; score= 7.4; -------scrCCGmyw-- ; cor=0.804; Ncor=0.483; logoDP=2.456; NsEucl=0.928; NSW=0.953; rcor=9; rNcor=3; rlogoDP=21; rNsEucl=2; rNSW=2; rank_mean=7.400; match_rank=4 a 0 0 0 0 0 0 0 21 22 61 2 3 6 35 22 32 0 0 c 0 0 0 0 0 0 0 28 42 0 95 91 0 31 38 24 0 0 g 0 0 0 0 0 0 0 27 18 39 3 2 86 12 15 16 0 0 t 0 0 0 0 0 0 0 24 18 0 0 4 8 22 25 28 0 0
ERF039_MA0995.1_JASPAR_rc_shift7 (ERF039:MA0995.1:JASPAR_rc)	0.838	0.471	2.438	0.923	0.946	2	5	22	4	5	7.600	6	; dyads_test_vs_ctrl_m1 versus ERF039_MA0995.1_JASPAR_rc (ERF039:MA0995.1:JASPAR_rc); m=6/28; ncol2=10; w=9; offset=6; strand=R; shift=7; score= 7.6; -------ycrCCGaCay- ; cor=0.838; Ncor=0.471; logoDP=2.438; NsEucl=0.923; NSW=0.946; rcor=2; rNcor=5; rlogoDP=22; rNsEucl=4; rNSW=5; rank_mean=7.600; match_rank=6 a 0 0 0 0 0 0 0 198 190 524 7 12 5 660 34 473 240 0 c 0 0 0 0 0 0 0 316 395 39 965 980 2 140 912 120 274 0 g 0 0 0 0 0 0 0 225 170 416 8 2 989 86 11 242 236 0 t 0 0 0 0 0 0 0 261 244 20 19 6 4 115 43 165 250 0