One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/02/compare-matrices_2019-07-02.131157_Jy6Cqb/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_2019-07-02.131157_Jy6Cqb/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m2_shift2 ; 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

oligos_5-8nt_m2_shift2 (oligos_5-8nt_m2)
; oligos_5-8nt_m2; m=0 (reference); ncol1=22; shift=2; ncol=24; --hkCcTTwTCCaCTCTCTstsyy ; Alignment reference a 0 0 9 8 3 4 2 3 18 2 0 1 17 1 0 0 2 1 3 1 2 4 5 7 c 0 0 12 6 25 21 1 4 4 4 25 31 4 30 2 29 0 29 2 10 7 12 12 15 g 0 0 3 10 2 1 6 0 1 1 4 1 5 1 1 1 1 3 2 16 3 10 3 0 t 0 0 9 9 3 7 24 26 10 26 4 0 7 1 30 3 30 0 26 6 21 7 13 11

AT4G00250.DAP_M0403_AthalianaCistrome_shift2 (AT4G00250.DAP:M0403:AthalianaCistrome) 0.786 0.465 4.284 0.922 0.920 1 1 2 1 1 1.200 1
; oligos_5-8nt_m2 versus AT4G00250.DAP_M0403_AthalianaCistrome (AT4G00250.DAP:M0403:AthalianaCistrome); m=1/4; ncol2=13; w=13; offset=0; strand=D; shift=2; score= 1.2; --wwycTTATCCAww--------- ; cor=0.786; Ncor=0.465; logoDP=4.284; NsEucl=0.922; NSW=0.920; rcor=1; rNcor=1; rlogoDP=2; rNsEucl=1; rNSW=1; rank_mean=1.200; match_rank=1 a 0 0 291 327 52 113 5 8 592 0 0 0 432 164 244 0 0 0 0 0 0 0 0 0 c 0 0 76 31 320 368 33 5 0 0 592 544 1 126 18 0 0 0 0 0 0 0 0 0 g 0 0 61 85 48 62 0 14 0 0 0 0 119 31 12 0 0 0 0 0 0 0 0 0 t 0 0 164 149 172 49 554 565 0 592 0 48 40 271 318 0 0 0 0 0 0 0 0 0

At5g47390_MA1398.1_JASPAR_shift0 (At5g47390:MA1398.1:JASPAR) 0.760 0.412 3.998 0.919 0.915 2 4 3 2 2 2.600 2
; oligos_5-8nt_m2 versus At5g47390_MA1398.1_JASPAR (At5g47390:MA1398.1:JASPAR); m=2/4; ncol2=15; w=13; offset=-2; strand=D; shift=0; score= 2.6; wwwwycTTATCCAww--------- ; cor=0.760; Ncor=0.412; logoDP=3.998; NsEucl=0.919; NSW=0.915; rcor=2; rNcor=4; rlogoDP=3; rNsEucl=2; rNSW=2; rank_mean=2.600; match_rank=2 a 225 190 277 290 76 136 11 11 599 0 0 0 441 214 305 0 0 0 0 0 0 0 0 0 c 119 122 73 45 285 300 44 6 0 0 599 527 4 126 16 0 0 0 0 0 0 0 0 0 g 52 67 63 92 48 57 0 15 0 0 0 0 74 28 9 0 0 0 0 0 0 0 0 0 t 203 220 186 172 190 106 544 567 0 599 0 72 80 231 269 0 0 0 0 0 0 0 0 0

At1g19000_MA1400.1_JASPAR_rc_shift2 (At1g19000:MA1400.1:JASPAR_rc) 0.717 0.456 1.410 0.914 0.897 3 2 4 3 3 3.000 3
; oligos_5-8nt_m2 versus At1g19000_MA1400.1_JASPAR_rc (At1g19000:MA1400.1:JASPAR_rc); m=3/4; ncol2=14; w=14; offset=0; strand=R; shift=2; score= 3; --wwycTTATCCAwww-------- ; cor=0.717; Ncor=0.456; logoDP=1.410; NsEucl=0.914; NSW=0.897; rcor=3; rNcor=2; rlogoDP=4; rNsEucl=3; rNSW=3; rank_mean=3.000; match_rank=3 a 0 0 273 304 47 123 12 6 599 0 0 0 484 154 243 232 0 0 0 0 0 0 0 0 c 0 0 86 48 319 338 33 5 0 0 599 570 1 136 28 73 0 0 0 0 0 0 0 0 g 0 0 71 86 61 56 0 8 0 0 0 0 81 27 9 22 0 0 0 0 0 0 0 0 t 0 0 169 161 172 82 554 580 0 599 0 29 33 282 319 272 0 0 0 0 0 0 0 0

At1g19000.ampDAP_M0590_AthalianaCistrome_shift2 (At1g19000.ampDAP:M0590:AthalianaCistrome) 0.712 0.453 4.551 0.913 0.893 4 3 1 4 4 3.200 4
; oligos_5-8nt_m2 versus At1g19000.ampDAP_M0590_AthalianaCistrome (At1g19000.ampDAP:M0590:AthalianaCistrome); m=4/4; ncol2=14; w=14; offset=0; strand=D; shift=2; score= 3.2; --wwycTTATCCAtww-------- ; cor=0.712; Ncor=0.453; logoDP=4.551; NsEucl=0.913; NSW=0.893; rcor=4; rNcor=3; rlogoDP=1; rNsEucl=4; rNSW=4; rank_mean=3.200; match_rank=4 a 0 0 303 280 53 102 5 5 599 0 0 0 493 148 243 242 0 0 0 0 0 0 0 0 c 0 0 73 52 309 340 14 6 0 0 599 568 0 129 23 69 0 0 0 0 0 0 0 0 g 0 0 61 95 58 81 0 1 0 0 0 0 71 32 12 21 0 0 0 0 0 0 0 0 t 0 0 162 172 179 76 580 587 0 599 0 31 35 290 321 267 0 0 0 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m2_shift2 (oligos_5-8nt_m2)													; oligos_5-8nt_m2; m=0 (reference); ncol1=22; shift=2; ncol=24; --hkCcTTwTCCaCTCTCTstsyy ; Alignment reference a 0 0 9 8 3 4 2 3 18 2 0 1 17 1 0 0 2 1 3 1 2 4 5 7 c 0 0 12 6 25 21 1 4 4 4 25 31 4 30 2 29 0 29 2 10 7 12 12 15 g 0 0 3 10 2 1 6 0 1 1 4 1 5 1 1 1 1 3 2 16 3 10 3 0 t 0 0 9 9 3 7 24 26 10 26 4 0 7 1 30 3 30 0 26 6 21 7 13 11
AT4G00250.DAP_M0403_AthalianaCistrome_shift2 (AT4G00250.DAP:M0403:AthalianaCistrome)	0.786	0.465	4.284	0.922	0.920	1	1	2	1	1	1.200	1	; oligos_5-8nt_m2 versus AT4G00250.DAP_M0403_AthalianaCistrome (AT4G00250.DAP:M0403:AthalianaCistrome); m=1/4; ncol2=13; w=13; offset=0; strand=D; shift=2; score= 1.2; --wwycTTATCCAww--------- ; cor=0.786; Ncor=0.465; logoDP=4.284; NsEucl=0.922; NSW=0.920; rcor=1; rNcor=1; rlogoDP=2; rNsEucl=1; rNSW=1; rank_mean=1.200; match_rank=1 a 0 0 291 327 52 113 5 8 592 0 0 0 432 164 244 0 0 0 0 0 0 0 0 0 c 0 0 76 31 320 368 33 5 0 0 592 544 1 126 18 0 0 0 0 0 0 0 0 0 g 0 0 61 85 48 62 0 14 0 0 0 0 119 31 12 0 0 0 0 0 0 0 0 0 t 0 0 164 149 172 49 554 565 0 592 0 48 40 271 318 0 0 0 0 0 0 0 0 0
At5g47390_MA1398.1_JASPAR_shift0 (At5g47390:MA1398.1:JASPAR)	0.760	0.412	3.998	0.919	0.915	2	4	3	2	2	2.600	2	; oligos_5-8nt_m2 versus At5g47390_MA1398.1_JASPAR (At5g47390:MA1398.1:JASPAR); m=2/4; ncol2=15; w=13; offset=-2; strand=D; shift=0; score= 2.6; wwwwycTTATCCAww--------- ; cor=0.760; Ncor=0.412; logoDP=3.998; NsEucl=0.919; NSW=0.915; rcor=2; rNcor=4; rlogoDP=3; rNsEucl=2; rNSW=2; rank_mean=2.600; match_rank=2 a 225 190 277 290 76 136 11 11 599 0 0 0 441 214 305 0 0 0 0 0 0 0 0 0 c 119 122 73 45 285 300 44 6 0 0 599 527 4 126 16 0 0 0 0 0 0 0 0 0 g 52 67 63 92 48 57 0 15 0 0 0 0 74 28 9 0 0 0 0 0 0 0 0 0 t 203 220 186 172 190 106 544 567 0 599 0 72 80 231 269 0 0 0 0 0 0 0 0 0
At1g19000_MA1400.1_JASPAR_rc_shift2 (At1g19000:MA1400.1:JASPAR_rc)	0.717	0.456	1.410	0.914	0.897	3	2	4	3	3	3.000	3	; oligos_5-8nt_m2 versus At1g19000_MA1400.1_JASPAR_rc (At1g19000:MA1400.1:JASPAR_rc); m=3/4; ncol2=14; w=14; offset=0; strand=R; shift=2; score= 3; --wwycTTATCCAwww-------- ; cor=0.717; Ncor=0.456; logoDP=1.410; NsEucl=0.914; NSW=0.897; rcor=3; rNcor=2; rlogoDP=4; rNsEucl=3; rNSW=3; rank_mean=3.000; match_rank=3 a 0 0 273 304 47 123 12 6 599 0 0 0 484 154 243 232 0 0 0 0 0 0 0 0 c 0 0 86 48 319 338 33 5 0 0 599 570 1 136 28 73 0 0 0 0 0 0 0 0 g 0 0 71 86 61 56 0 8 0 0 0 0 81 27 9 22 0 0 0 0 0 0 0 0 t 0 0 169 161 172 82 554 580 0 599 0 29 33 282 319 272 0 0 0 0 0 0 0 0
At1g19000.ampDAP_M0590_AthalianaCistrome_shift2 (At1g19000.ampDAP:M0590:AthalianaCistrome)	0.712	0.453	4.551	0.913	0.893	4	3	1	4	4	3.200	4	; oligos_5-8nt_m2 versus At1g19000.ampDAP_M0590_AthalianaCistrome (At1g19000.ampDAP:M0590:AthalianaCistrome); m=4/4; ncol2=14; w=14; offset=0; strand=D; shift=2; score= 3.2; --wwycTTATCCAtww-------- ; cor=0.712; Ncor=0.453; logoDP=4.551; NsEucl=0.913; NSW=0.893; rcor=4; rNcor=3; rlogoDP=1; rNsEucl=4; rNSW=4; rank_mean=3.200; match_rank=4 a 0 0 303 280 53 102 5 5 599 0 0 0 493 148 243 242 0 0 0 0 0 0 0 0 c 0 0 73 52 309 340 14 6 0 0 599 568 0 129 23 69 0 0 0 0 0 0 0 0 g 0 0 61 95 58 81 0 1 0 0 0 0 71 32 12 21 0 0 0 0 0 0 0 0 t 0 0 162 172 179 76 580 587 0 599 0 31 35 290 321 267 0 0 0 0 0 0 0 0