One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/02/compare-matrices_2019-07-02.130441_aXfMWy/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_2019-07-02.130441_aXfMWy/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m3_shift0 ; 9 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

oligos_5-8nt_m3_shift0 (oligos_5-8nt_m3)
; oligos_5-8nt_m3; m=0 (reference); ncol1=13; shift=0; ncol=19; wwwTTGGGCCaww------ ; Alignment reference a 340 365 479 133 38 48 46 81 22 40 770 428 367 0 0 0 0 0 0 c 246 179 170 65 21 14 19 66 1068 1043 90 221 232 0 0 0 0 0 0 g 234 236 180 87 29 1058 1060 958 20 10 100 182 268 0 0 0 0 0 0 t 343 383 334 878 1075 43 38 58 53 70 203 332 296 0 0 0 0 0 0

LOC_Os02g42380_M1657_1.02_CISBP_shift3 (LOC_Os02g42380:M1657_1.02:CISBP) 0.721 0.554 3.953 0.898 0.896 3 1 3 2 2 2.200 1
; oligos_5-8nt_m3 versus LOC_Os02g42380_M1657_1.02_CISBP (LOC_Os02g42380:M1657_1.02:CISBP); m=1/8; ncol2=10; w=10; offset=3; strand=D; shift=3; score= 2.2; ---kkGGgcCCmm------ ; cor=0.721; Ncor=0.554; logoDP=3.953; NsEucl=0.898; NSW=0.896; rcor=3; rNcor=1; rlogoDP=3; rNsEucl=2; rNSW=2; rank_mean=2.200; match_rank=1 a 0 0 0 18 7 0 0.0000 13 11 0.0000 7 45 28 0 0 0 0 0 0 c 0 0 0 13 15 0 0.0000 10 66 1.0000 93 33 41 0 0 0 0 0 0 g 0 0 0 41 33 93 1.0000 66 10 0.0000 0 15 13 0 0 0 0 0 0 t 0 0 0 28 45 7 0.0000 11 13 0.0000 0 7 18 0 0 0 0 0 0

OJ1581_MA1031.1_JASPAR_shift3 (OJ1581:MA1031.1:JASPAR) 0.719 0.553 3.948 0.898 0.895 4 2 4 4 4 3.600 2
; oligos_5-8nt_m3 versus OJ1581_MA1031.1_JASPAR (OJ1581:MA1031.1:JASPAR); m=2/8; ncol2=10; w=10; offset=3; strand=D; shift=3; score= 3.6; ---kkGGgcCCmm------ ; cor=0.719; Ncor=0.553; logoDP=3.948; NsEucl=0.898; NSW=0.895; rcor=4; rNcor=2; rlogoDP=4; rNsEucl=4; rNSW=4; rank_mean=3.600; match_rank=2 a 0 0 0 175 74 0 0 127 112 0 71 445 279 0 0 0 0 0 0 c 0 0 0 131 146 0 0 101 661 1000 929 335 414 0 0 0 0 0 0 g 0 0 0 414 335 929 1000 661 101 0 0 146 131 0 0 0 0 0 0 t 0 0 0 279 445 71 0 112 127 0 0 74 175 0 0 0 0 0 0

TCP3_M1645_1.02_CISBP_rc_shift2 (TCP3:M1645_1.02:CISBP_rc) 0.719 0.553 1.920 0.898 0.895 5 3 7 3 3 4.200 3
; oligos_5-8nt_m3 versus TCP3_M1645_1.02_CISBP_rc (TCP3:M1645_1.02:CISBP_rc); m=3/8; ncol2=10; w=10; offset=2; strand=R; shift=2; score= 4.2; --dgTGGtCCcm------- ; cor=0.719; Ncor=0.553; logoDP=1.920; NsEucl=0.898; NSW=0.895; rcor=5; rNcor=3; rlogoDP=7; rNsEucl=3; rNSW=3; rank_mean=4.200; match_rank=3 a 0 0 26 14 2 0 0 11 5 4 20 28 0 0 0 0 0 0 0 c 0 0 16 11 11 0 2 3 80 91 58 31 0 0 0 0 0 0 0 g 0 0 29 67 7 97 96 24 12 2 5 24 0 0 0 0 0 0 0 t 0 0 29 8 80 3 2 62 3 3 17 17 0 0 0 0 0 0 0

AT5G61850.1_LEAFY_EEADannot_rc_shift0 (AT5G61850.1:LEAFY:EEADannot_rc) 0.701 0.479 0.513 0.916 0.908 8 4 8 1 1 4.400 5
; oligos_5-8nt_m3 versus AT5G61850.1_LEAFY_EEADannot_rc (AT5G61850.1:LEAFY:EEADannot_rc); m=5/8; ncol2=19; w=13; offset=0; strand=R; shift=0; score= 4.4; wwtwTkGwCCrtTGGwyhw ; cor=0.701; Ncor=0.479; logoDP=0.513; NsEucl=0.916; NSW=0.908; rcor=8; rNcor=4; rlogoDP=8; rNsEucl=1; rNSW=1; rank_mean=4.400; match_rank=5 a 111 96 50 144 27 21 35 208 7 7 166 62 15 22 10 151 17 107 144 c 65 66 62 5 24 3 2 15 353 333 6 43 24 3 3 5 235 128 55 g 80 65 39 13 16 223 327 6 2 2 151 18 8 342 349 24 11 26 57 t 116 145 221 210 305 125 8 143 10 30 49 249 325 5 10 192 109 111 116

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m3_shift0 (oligos_5-8nt_m3)													; oligos_5-8nt_m3; m=0 (reference); ncol1=13; shift=0; ncol=19; wwwTTGGGCCaww------ ; Alignment reference a 340 365 479 133 38 48 46 81 22 40 770 428 367 0 0 0 0 0 0 c 246 179 170 65 21 14 19 66 1068 1043 90 221 232 0 0 0 0 0 0 g 234 236 180 87 29 1058 1060 958 20 10 100 182 268 0 0 0 0 0 0 t 343 383 334 878 1075 43 38 58 53 70 203 332 296 0 0 0 0 0 0
LOC_Os02g42380_M1657_1.02_CISBP_shift3 (LOC_Os02g42380:M1657_1.02:CISBP)	0.721	0.554	3.953	0.898	0.896	3	1	3	2	2	2.200	1	; oligos_5-8nt_m3 versus LOC_Os02g42380_M1657_1.02_CISBP (LOC_Os02g42380:M1657_1.02:CISBP); m=1/8; ncol2=10; w=10; offset=3; strand=D; shift=3; score= 2.2; ---kkGGgcCCmm------ ; cor=0.721; Ncor=0.554; logoDP=3.953; NsEucl=0.898; NSW=0.896; rcor=3; rNcor=1; rlogoDP=3; rNsEucl=2; rNSW=2; rank_mean=2.200; match_rank=1 a 0 0 0 18 7 0 0.0000 13 11 0.0000 7 45 28 0 0 0 0 0 0 c 0 0 0 13 15 0 0.0000 10 66 1.0000 93 33 41 0 0 0 0 0 0 g 0 0 0 41 33 93 1.0000 66 10 0.0000 0 15 13 0 0 0 0 0 0 t 0 0 0 28 45 7 0.0000 11 13 0.0000 0 7 18 0 0 0 0 0 0
OJ1581_MA1031.1_JASPAR_shift3 (OJ1581:MA1031.1:JASPAR)	0.719	0.553	3.948	0.898	0.895	4	2	4	4	4	3.600	2	; oligos_5-8nt_m3 versus OJ1581_MA1031.1_JASPAR (OJ1581:MA1031.1:JASPAR); m=2/8; ncol2=10; w=10; offset=3; strand=D; shift=3; score= 3.6; ---kkGGgcCCmm------ ; cor=0.719; Ncor=0.553; logoDP=3.948; NsEucl=0.898; NSW=0.895; rcor=4; rNcor=2; rlogoDP=4; rNsEucl=4; rNSW=4; rank_mean=3.600; match_rank=2 a 0 0 0 175 74 0 0 127 112 0 71 445 279 0 0 0 0 0 0 c 0 0 0 131 146 0 0 101 661 1000 929 335 414 0 0 0 0 0 0 g 0 0 0 414 335 929 1000 661 101 0 0 146 131 0 0 0 0 0 0 t 0 0 0 279 445 71 0 112 127 0 0 74 175 0 0 0 0 0 0
TCP3_M1645_1.02_CISBP_rc_shift2 (TCP3:M1645_1.02:CISBP_rc)	0.719	0.553	1.920	0.898	0.895	5	3	7	3	3	4.200	3	; oligos_5-8nt_m3 versus TCP3_M1645_1.02_CISBP_rc (TCP3:M1645_1.02:CISBP_rc); m=3/8; ncol2=10; w=10; offset=2; strand=R; shift=2; score= 4.2; --dgTGGtCCcm------- ; cor=0.719; Ncor=0.553; logoDP=1.920; NsEucl=0.898; NSW=0.895; rcor=5; rNcor=3; rlogoDP=7; rNsEucl=3; rNSW=3; rank_mean=4.200; match_rank=3 a 0 0 26 14 2 0 0 11 5 4 20 28 0 0 0 0 0 0 0 c 0 0 16 11 11 0 2 3 80 91 58 31 0 0 0 0 0 0 0 g 0 0 29 67 7 97 96 24 12 2 5 24 0 0 0 0 0 0 0 t 0 0 29 8 80 3 2 62 3 3 17 17 0 0 0 0 0 0 0
AT5G61850.1_LEAFY_EEADannot_rc_shift0 (AT5G61850.1:LEAFY:EEADannot_rc)	0.701	0.479	0.513	0.916	0.908	8	4	8	1	1	4.400	5	; oligos_5-8nt_m3 versus AT5G61850.1_LEAFY_EEADannot_rc (AT5G61850.1:LEAFY:EEADannot_rc); m=5/8; ncol2=19; w=13; offset=0; strand=R; shift=0; score= 4.4; wwtwTkGwCCrtTGGwyhw ; cor=0.701; Ncor=0.479; logoDP=0.513; NsEucl=0.916; NSW=0.908; rcor=8; rNcor=4; rlogoDP=8; rNsEucl=1; rNSW=1; rank_mean=4.400; match_rank=5 a 111 96 50 144 27 21 35 208 7 7 166 62 15 22 10 151 17 107 144 c 65 66 62 5 24 3 2 15 353 333 6 43 24 3 3 5 235 128 55 g 80 65 39 13 16 223 327 6 2 2 151 18 8 342 349 24 11 26 57 t 116 145 221 210 305 125 8 143 10 30 49 249 325 5 10 192 109 111 116