One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 11/regulon11.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o 11/regulon11.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift2 ; 6 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
dyads_test_vs_ctrl_m1_shift2 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=2; ncol=16; --bwGTTbtwtCAAam ; Alignment reference a 0 0 3 8 0 0 0 5 4 9 5 0 23 23 10 9 c 0 0 6 5 0 0 0 6 5 3 4 23 0 0 3 6 g 0 0 7 3 23 0 0 6 4 5 5 0 0 0 5 3 t 0 0 7 7 0 23 23 6 10 6 9 0 0 0 5 5

MYBAS1_M00798_TRANSFAC_rc_shift0 (MYBAS1_M00798_TRANSFAC_rc) 0.884 0.497 0.018 -0.070 0.940 0.587 0.967 2 1 6 5 1 2 1 2.571 1
; dyads_test_vs_ctrl_m1 versus MYBAS1_M00798_TRANSFAC_rc; m=1/5; ncol2=11; w=9; offset=-2; strand=R; shift=0; score= 2.5714; rgcmGTTrbsg----- ; cor=0.884; Ncor=0.497; logoDP=0.018; NIcor=-0.070; NsEucl=0.940; SSD=0.587; NSW=0.967; rcor=2; rNcor=1; rlogoDP=6; rNIcor=5; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=2.571; match_rank=1 a 8 4 4 6 0 0 0 9 2 2 2 0 0 0 0 0 c 0 3 9 6 0 0 0 2 5 5 4 0 0 0 0 0 g 8 9 4 4 20 0 0 9 6 7 7 0 0 0 0 0 t 2 3 2 3 0 20 20 0 5 4 4 0 0 0 0 0

MYB2_MYB2_Athamap_rc_shift1 (MYB2_MYB2_Athamap_rc) 0.899 0.419 0.285 -0.026 0.926 0.531 0.962 1 5 3 3 3 1 2 2.571 2
; dyads_test_vs_ctrl_m1 versus MYB2_MYB2_Athamap_rc; m=2/5; ncol2=8; w=7; offset=-1; strand=R; shift=1; score= 2.5714; -kbvGTTdb------- ; cor=0.899; Ncor=0.419; logoDP=0.285; NIcor=-0.026; NsEucl=0.926; SSD=0.531; NSW=0.962; rcor=1; rNcor=5; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=1; rNSW=2; rank_mean=2.571; match_rank=2 a 0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 c 0 0 2 1 0 0 0 0 1 0 0 0 0 0 0 0 g 0 2 1 1 4 0 0 1 2 0 0 0 0 0 0 0 t 0 2 1 0 0 4 4 1 1 0 0 0 0 0 0 0

ZFP5_M0369_1.02_CISBP_rc_shift3 (ZFP5_M0369_1.02_CISBP_rc) 0.817 0.467 0.031 -0.049 0.917 0.880 0.945 3 3 5 4 4 3 3 3.571 4
; dyads_test_vs_ctrl_m1 versus ZFP5_M0369_1.02_CISBP_rc; m=3/5; ncol2=8; w=8; offset=1; strand=R; shift=3; score= 3.5714; ---aswThvmw----- ; cor=0.817; Ncor=0.467; logoDP=0.031; NIcor=-0.049; NsEucl=0.917; SSD=0.880; NSW=0.945; rcor=3; rNcor=3; rlogoDP=5; rNIcor=4; rNsEucl=4; rSSD=3; rNSW=3; rank_mean=3.571; match_rank=4 a 0 0 0 53 1 28 11 25 27 28 26 0 0 0 0 0 c 0 0 0 6 41 6 9 31 25 27 24 0 0 0 0 0 g 0 0 0 22 53 0 5 18 25 24 24 0 0 0 0 0 t 0 0 0 19 5 66 75 26 23 21 26 0 0 0 0 0

ZFP8_M0371_1.02_CISBP_shift3 (ZFP8_M0371_1.02_CISBP) 0.764 0.491 1.129 0.510 0.902 1.556 0.914 5 2 2 1 6 5 6 3.857 5
; dyads_test_vs_ctrl_m1 versus ZFP8_M0371_1.02_CISBP; m=4/5; ncol2=9; w=9; offset=1; strand=D; shift=3; score= 3.8571; ---wswthvmdy---- ; cor=0.764; Ncor=0.491; logoDP=1.129; NIcor=0.510; NsEucl=0.902; SSD=1.556; NSW=0.914; rcor=5; rNcor=2; rlogoDP=2; rNIcor=1; rNsEucl=6; rSSD=5; rNSW=6; rank_mean=3.857; match_rank=5 a 0 0 0 46 4 27 14 26 27 27 25 24 0 0 0 0 c 0 0 0 14 32 8 10 29 25 26 23 25 0 0 0 0 g 0 0 0 14 56 0 10 19 25 24 26 22 0 0 0 0 t 0 0 0 26 8 65 66 26 23 23 26 29 0 0 0 0

Gam1_MA0034.1_JASPAR_rc_shift0 (Gam1_MA0034.1_JASPAR_rc) 0.808 0.404 0.073 -0.084 0.911 1.011 0.937 4 6 4 6 5 4 5 4.857 6
; dyads_test_vs_ctrl_m1 versus Gam1_MA0034.1_JASPAR_rc; m=5/5; ncol2=10; w=8; offset=-2; strand=R; shift=0; score= 4.8571; GkCgGTTryc------ ; cor=0.808; Ncor=0.404; logoDP=0.073; NIcor=-0.084; NsEucl=0.911; SSD=1.011; NSW=0.937; rcor=4; rNcor=6; rlogoDP=4; rNIcor=6; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=4.857; match_rank=6 a 0 4 0 2 0 0 0 9 3 4 0 0 0 0 0 0 c 1 0 19 6 0 0 1 0 7 11 0 0 0 0 0 0 g 19 11 0 14 24 0 1 13 5 6 0 0 0 0 0 0 t 5 10 6 3 1 25 23 3 10 4 0 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m1_shift2 (dyads_test_vs_ctrl_m1)																	; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=2; ncol=16; --bwGTTbtwtCAAam ; Alignment reference a 0 0 3 8 0 0 0 5 4 9 5 0 23 23 10 9 c 0 0 6 5 0 0 0 6 5 3 4 23 0 0 3 6 g 0 0 7 3 23 0 0 6 4 5 5 0 0 0 5 3 t 0 0 7 7 0 23 23 6 10 6 9 0 0 0 5 5
MYBAS1_M00798_TRANSFAC_rc_shift0 (MYBAS1_M00798_TRANSFAC_rc)	0.884	0.497	0.018	-0.070	0.940	0.587	0.967	2	1	6	5	1	2	1	2.571	1	; dyads_test_vs_ctrl_m1 versus MYBAS1_M00798_TRANSFAC_rc; m=1/5; ncol2=11; w=9; offset=-2; strand=R; shift=0; score= 2.5714; rgcmGTTrbsg----- ; cor=0.884; Ncor=0.497; logoDP=0.018; NIcor=-0.070; NsEucl=0.940; SSD=0.587; NSW=0.967; rcor=2; rNcor=1; rlogoDP=6; rNIcor=5; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=2.571; match_rank=1 a 8 4 4 6 0 0 0 9 2 2 2 0 0 0 0 0 c 0 3 9 6 0 0 0 2 5 5 4 0 0 0 0 0 g 8 9 4 4 20 0 0 9 6 7 7 0 0 0 0 0 t 2 3 2 3 0 20 20 0 5 4 4 0 0 0 0 0
MYB2_MYB2_Athamap_rc_shift1 (MYB2_MYB2_Athamap_rc)	0.899	0.419	0.285	-0.026	0.926	0.531	0.962	1	5	3	3	3	1	2	2.571	2	; dyads_test_vs_ctrl_m1 versus MYB2_MYB2_Athamap_rc; m=2/5; ncol2=8; w=7; offset=-1; strand=R; shift=1; score= 2.5714; -kbvGTTdb------- ; cor=0.899; Ncor=0.419; logoDP=0.285; NIcor=-0.026; NsEucl=0.926; SSD=0.531; NSW=0.962; rcor=1; rNcor=5; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=1; rNSW=2; rank_mean=2.571; match_rank=2 a 0 0 0 2 0 0 0 2 0 0 0 0 0 0 0 0 c 0 0 2 1 0 0 0 0 1 0 0 0 0 0 0 0 g 0 2 1 1 4 0 0 1 2 0 0 0 0 0 0 0 t 0 2 1 0 0 4 4 1 1 0 0 0 0 0 0 0
ZFP5_M0369_1.02_CISBP_rc_shift3 (ZFP5_M0369_1.02_CISBP_rc)	0.817	0.467	0.031	-0.049	0.917	0.880	0.945	3	3	5	4	4	3	3	3.571	4	; dyads_test_vs_ctrl_m1 versus ZFP5_M0369_1.02_CISBP_rc; m=3/5; ncol2=8; w=8; offset=1; strand=R; shift=3; score= 3.5714; ---aswThvmw----- ; cor=0.817; Ncor=0.467; logoDP=0.031; NIcor=-0.049; NsEucl=0.917; SSD=0.880; NSW=0.945; rcor=3; rNcor=3; rlogoDP=5; rNIcor=4; rNsEucl=4; rSSD=3; rNSW=3; rank_mean=3.571; match_rank=4 a 0 0 0 53 1 28 11 25 27 28 26 0 0 0 0 0 c 0 0 0 6 41 6 9 31 25 27 24 0 0 0 0 0 g 0 0 0 22 53 0 5 18 25 24 24 0 0 0 0 0 t 0 0 0 19 5 66 75 26 23 21 26 0 0 0 0 0
ZFP8_M0371_1.02_CISBP_shift3 (ZFP8_M0371_1.02_CISBP)	0.764	0.491	1.129	0.510	0.902	1.556	0.914	5	2	2	1	6	5	6	3.857	5	; dyads_test_vs_ctrl_m1 versus ZFP8_M0371_1.02_CISBP; m=4/5; ncol2=9; w=9; offset=1; strand=D; shift=3; score= 3.8571; ---wswthvmdy---- ; cor=0.764; Ncor=0.491; logoDP=1.129; NIcor=0.510; NsEucl=0.902; SSD=1.556; NSW=0.914; rcor=5; rNcor=2; rlogoDP=2; rNIcor=1; rNsEucl=6; rSSD=5; rNSW=6; rank_mean=3.857; match_rank=5 a 0 0 0 46 4 27 14 26 27 27 25 24 0 0 0 0 c 0 0 0 14 32 8 10 29 25 26 23 25 0 0 0 0 g 0 0 0 14 56 0 10 19 25 24 26 22 0 0 0 0 t 0 0 0 26 8 65 66 26 23 23 26 29 0 0 0 0
Gam1_MA0034.1_JASPAR_rc_shift0 (Gam1_MA0034.1_JASPAR_rc)	0.808	0.404	0.073	-0.084	0.911	1.011	0.937	4	6	4	6	5	4	5	4.857	6	; dyads_test_vs_ctrl_m1 versus Gam1_MA0034.1_JASPAR_rc; m=5/5; ncol2=10; w=8; offset=-2; strand=R; shift=0; score= 4.8571; GkCgGTTryc------ ; cor=0.808; Ncor=0.404; logoDP=0.073; NIcor=-0.084; NsEucl=0.911; SSD=1.011; NSW=0.937; rcor=4; rNcor=6; rlogoDP=4; rNIcor=6; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=4.857; match_rank=6 a 0 4 0 2 0 0 0 9 3 4 0 0 0 0 0 0 c 1 0 19 6 0 0 1 0 7 11 0 0 0 0 0 0 g 19 11 0 14 24 0 1 13 5 6 0 0 0 0 0 0 t 5 10 6 3 1 25 23 3 10 4 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m2_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
dyads_test_vs_ctrl_m2_shift0 (dyads_test_vs_ctrl_m2)
; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=23; shift=0; ncol=23; hhAAAkwwmwwtwAmwwdAAcvw ; Alignment reference a 10 9 26 27 31 1 8 11 8 12 12 7 14 26 20 12 14 8 31 25 4 8 10 c 8 12 2 1 1 1 5 0 11 5 7 6 6 2 8 5 4 5 1 3 21 9 4 g 4 3 0 2 0 13 1 6 6 3 5 4 2 2 2 7 4 9 0 0 2 9 7 t 10 8 4 2 0 17 18 15 7 12 8 15 10 2 2 8 10 10 0 4 5 6 11

PK22848.1_M0587_1.02_CISBP_shift0 (PK22848.1_M0587_1.02_CISBP) 0.755 0.427 2.066 0.409 0.932 1.579 0.939 6 4 1 2 2 6 4 3.571 3
; dyads_test_vs_ctrl_m2 versus PK22848.1_M0587_1.02_CISBP; m=1/1; ncol2=13; w=13; offset=0; strand=D; shift=0; score= 3.5714; mmAAATTTwaawa---------- ; cor=0.755; Ncor=0.427; logoDP=2.066; NIcor=0.409; NsEucl=0.932; SSD=1.579; NSW=0.939; rcor=6; rNcor=4; rlogoDP=1; rNIcor=2; rNsEucl=2; rSSD=6; rNSW=4; rank_mean=3.571; match_rank=3 a 29 27 68 79 82 0 0 0 26 63 58 39 35 0 0 0 0 0 0 0 0 0 0 c 29 25 11 7 3 0 0 0 13 9 14 17 21 0 0 0 0 0 0 0 0 0 0 g 21 24 11 7 3 0 0 8 13 18 14 18 22 0 0 0 0 0 0 0 0 0 0 t 21 24 10 7 12 100 100 92 48 10 14 26 22 0 0 0 0 0 0 0 0 0 0