One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.165756_scTDUg/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_2019-07-04.165756_scTDUg/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift10 ; 147 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_shift10 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=11; shift=10; ncol=21; ----------wtACACGTAtm ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 129 107 375 19 398 30 28 14 299 94 133 c 0 0 0 0 0 0 0 0 0 0 77 93 25 390 7 363 10 20 27 87 115 g 0 0 0 0 0 0 0 0 0 0 89 95 12 8 17 10 385 4 77 93 79 t 0 0 0 0 0 0 0 0 0 0 137 137 20 15 10 29 9 394 29 158 105

ABI5_M0261_1.02_CISBP_shift10 (ABI5:M0261_1.02:CISBP) 0.869 0.790 5.854 0.927 0.946 7 3 17 9 10 9.200 1
; dyads_test_vs_ctrl_m1 versus ABI5_M0261_1.02_CISBP (ABI5:M0261_1.02:CISBP); m=1/146; ncol2=10; w=10; offset=0; strand=D; shift=10; score= 9.2; ----------bgmCACGTGk- ; cor=0.869; Ncor=0.790; logoDP=5.854; NsEucl=0.927; NSW=0.946; rcor=7; rNcor=3; rlogoDP=17; rNsEucl=9; rNSW=10; rank_mean=9.200; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 18 9 61 0 100 0 0 0 15 16 0 c 0 0 0 0 0 0 0 0 0 0 26 9 31 92 0 100 0 0 7 16 0 g 0 0 0 0 0 0 0 0 0 0 25 65 0 8 0 0 100 0 71 34 0 t 0 0 0 0 0 0 0 0 0 0 31 17 8 0 0 0 0 100 7 34 0

ANAC55_ANAC55_ArabidopsisPBM_shift11 (ANAC55:ANAC55:ArabidopsisPBM) 0.891 0.810 4.389 0.933 0.955 5 2 49 5 5 13.200 5
; dyads_test_vs_ctrl_m1 versus ANAC55_ANAC55_ArabidopsisPBM (ANAC55:ANAC55:ArabidopsisPBM); m=5/146; ncol2=10; w=10; offset=1; strand=D; shift=11; score= 13.2; -----------wACACGTAAy ; cor=0.891; Ncor=0.810; logoDP=4.389; NsEucl=0.933; NSW=0.955; rcor=5; rNcor=2; rlogoDP=49; rNsEucl=5; rNSW=5; rank_mean=13.200; match_rank=5 a 0 0 0 0 0 0 0 0 0 0 0 36 80 2 97 2 1 1 88 87 9 c 0 0 0 0 0 0 0 0 0 0 0 19 3 77 2 96 2 12 8 1 40 g 0 0 0 0 0 0 0 0 0 0 0 15 4 2 0 1 95 13 0 0 10 t 0 0 0 0 0 0 0 0 0 0 0 30 13 19 1 1 2 74 4 12 41

ABF1_M0257_1.02_CISBP_shift10 (ABF1:M0257_1.02:CISBP) 0.861 0.861 3.251 0.938 0.958 9 1 84 4 4 20.400 6
; dyads_test_vs_ctrl_m1 versus ABF1_M0257_1.02_CISBP (ABF1:M0257_1.02:CISBP); m=6/146; ncol2=11; w=11; offset=0; strand=D; shift=10; score= 20.4; ----------gdACACGTGkb ; cor=0.861; Ncor=0.861; logoDP=3.251; NsEucl=0.938; NSW=0.958; rcor=9; rNcor=1; rlogoDP=84; rNsEucl=4; rNSW=4; rank_mean=20.400; match_rank=6 a 0 0 0 0 0 0 0 0 0 0 21 26 68 16 73 0 18 0 12 16 18 c 0 0 0 0 0 0 0 0 0 0 21 16 18 75 8 91 0 10 4 19 28 g 0 0 0 0 0 0 0 0 0 0 37 33 7 0 10 0 82 0 71 40 28 t 0 0 0 0 0 0 0 0 0 0 21 25 7 9 9 9 0 90 13 25 26

AT4G18890_MA1333.1_JASPAR_rc_shift10 (AT4G18890:MA1333.1:JASPAR_rc) 0.789 0.789 0.249 0.908 0.907 44 5 128 59 71 61.400
; dyads_test_vs_ctrl_m1 versus AT4G18890_MA1333.1_JASPAR_rc (AT4G18890:MA1333.1:JASPAR_rc); m=54/146; ncol2=11; w=11; offset=0; strand=R; shift=10; score= 61.4; ----------ycACACGTGyr ; cor=0.789; Ncor=0.789; logoDP=0.249; NsEucl=0.908; NSW=0.907; rcor=44; rNcor=5; rlogoDP=128; rNsEucl=59; rNSW=71; rank_mean=61.400; match_rank= a 0 0 0 0 0 0 0 0 0 0 81 52 405 0 589 0 0 0 1 0 225 c 0 0 0 0 0 0 0 0 0 0 179 338 60 590 0 589 0 0 0 383 43 g 0 0 0 0 0 0 0 0 0 0 91 140 74 0 0 0 590 0 589 28 319 t 0 0 0 0 0 0 0 0 0 0 239 60 51 0 1 1 0 590 0 179 3

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m1_shift10 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=11; shift=10; ncol=21; ----------wtACACGTAtm ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 129 107 375 19 398 30 28 14 299 94 133 c 0 0 0 0 0 0 0 0 0 0 77 93 25 390 7 363 10 20 27 87 115 g 0 0 0 0 0 0 0 0 0 0 89 95 12 8 17 10 385 4 77 93 79 t 0 0 0 0 0 0 0 0 0 0 137 137 20 15 10 29 9 394 29 158 105
ABI5_M0261_1.02_CISBP_shift10 (ABI5:M0261_1.02:CISBP)	0.869	0.790	5.854	0.927	0.946	7	3	17	9	10	9.200	1	; dyads_test_vs_ctrl_m1 versus ABI5_M0261_1.02_CISBP (ABI5:M0261_1.02:CISBP); m=1/146; ncol2=10; w=10; offset=0; strand=D; shift=10; score= 9.2; ----------bgmCACGTGk- ; cor=0.869; Ncor=0.790; logoDP=5.854; NsEucl=0.927; NSW=0.946; rcor=7; rNcor=3; rlogoDP=17; rNsEucl=9; rNSW=10; rank_mean=9.200; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 18 9 61 0 100 0 0 0 15 16 0 c 0 0 0 0 0 0 0 0 0 0 26 9 31 92 0 100 0 0 7 16 0 g 0 0 0 0 0 0 0 0 0 0 25 65 0 8 0 0 100 0 71 34 0 t 0 0 0 0 0 0 0 0 0 0 31 17 8 0 0 0 0 100 7 34 0
ANAC55_ANAC55_ArabidopsisPBM_shift11 (ANAC55:ANAC55:ArabidopsisPBM)	0.891	0.810	4.389	0.933	0.955	5	2	49	5	5	13.200	5	; dyads_test_vs_ctrl_m1 versus ANAC55_ANAC55_ArabidopsisPBM (ANAC55:ANAC55:ArabidopsisPBM); m=5/146; ncol2=10; w=10; offset=1; strand=D; shift=11; score= 13.2; -----------wACACGTAAy ; cor=0.891; Ncor=0.810; logoDP=4.389; NsEucl=0.933; NSW=0.955; rcor=5; rNcor=2; rlogoDP=49; rNsEucl=5; rNSW=5; rank_mean=13.200; match_rank=5 a 0 0 0 0 0 0 0 0 0 0 0 36 80 2 97 2 1 1 88 87 9 c 0 0 0 0 0 0 0 0 0 0 0 19 3 77 2 96 2 12 8 1 40 g 0 0 0 0 0 0 0 0 0 0 0 15 4 2 0 1 95 13 0 0 10 t 0 0 0 0 0 0 0 0 0 0 0 30 13 19 1 1 2 74 4 12 41
ABF1_M0257_1.02_CISBP_shift10 (ABF1:M0257_1.02:CISBP)	0.861	0.861	3.251	0.938	0.958	9	1	84	4	4	20.400	6	; dyads_test_vs_ctrl_m1 versus ABF1_M0257_1.02_CISBP (ABF1:M0257_1.02:CISBP); m=6/146; ncol2=11; w=11; offset=0; strand=D; shift=10; score= 20.4; ----------gdACACGTGkb ; cor=0.861; Ncor=0.861; logoDP=3.251; NsEucl=0.938; NSW=0.958; rcor=9; rNcor=1; rlogoDP=84; rNsEucl=4; rNSW=4; rank_mean=20.400; match_rank=6 a 0 0 0 0 0 0 0 0 0 0 21 26 68 16 73 0 18 0 12 16 18 c 0 0 0 0 0 0 0 0 0 0 21 16 18 75 8 91 0 10 4 19 28 g 0 0 0 0 0 0 0 0 0 0 37 33 7 0 10 0 82 0 71 40 28 t 0 0 0 0 0 0 0 0 0 0 21 25 7 9 9 9 0 90 13 25 26
AT4G18890_MA1333.1_JASPAR_rc_shift10 (AT4G18890:MA1333.1:JASPAR_rc)	0.789	0.789	0.249	0.908	0.907	44	5	128	59	71	61.400		; dyads_test_vs_ctrl_m1 versus AT4G18890_MA1333.1_JASPAR_rc (AT4G18890:MA1333.1:JASPAR_rc); m=54/146; ncol2=11; w=11; offset=0; strand=R; shift=10; score= 61.4; ----------ycACACGTGyr ; cor=0.789; Ncor=0.789; logoDP=0.249; NsEucl=0.908; NSW=0.907; rcor=44; rNcor=5; rlogoDP=128; rNsEucl=59; rNSW=71; rank_mean=61.400; match_rank= a 0 0 0 0 0 0 0 0 0 0 81 52 405 0 589 0 0 0 1 0 225 c 0 0 0 0 0 0 0 0 0 0 179 338 60 590 0 589 0 0 0 383 43 g 0 0 0 0 0 0 0 0 0 0 91 140 74 0 0 0 590 0 589 28 319 t 0 0 0 0 0 0 0 0 0 0 239 60 51 0 1 1 0 590 0 179 3