One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/03/compare-matrices_2019-07-03.153415_PKe73D/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/2019/07/03/compare-matrices_2019-07-03.153415_PKe73D/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift8 ; 108 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_m1_shift8 (oligos_5-8nt_m1)
; oligos_5-8nt_m1; m=0 (reference); ncol1=16; shift=8; ncol=24; --------wwtGACACGTGTCaww ; Alignment reference a 0 0 0 0 0 0 0 0 88 90 55 29 236 24 291 15 18 11 18 24 39 155 101 103 c 0 0 0 0 0 0 0 0 68 64 57 22 45 263 2 271 8 11 7 8 217 45 58 58 g 0 0 0 0 0 0 0 0 62 61 46 227 7 7 9 9 274 2 267 49 24 58 66 66 t 0 0 0 0 0 0 0 0 95 98 155 35 25 19 11 18 13 289 21 232 33 55 88 86

HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR) 0.949 0.949 6.807 0.965 0.980 7 1 8 1 3 4.000 1
; oligos_5-8nt_m1 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=1/107; ncol2=16; w=16; offset=0; strand=D; shift=8; score= 4; --------wwtGmCACGTGkCaww ; cor=0.949; Ncor=0.949; logoDP=6.807; NsEucl=0.965; NSW=0.980; rcor=7; rNcor=1; rlogoDP=8; rNsEucl=1; rNSW=3; rank_mean=4.000; match_rank=1 a 0 0 0 0 0 0 0 0 103 108 52 9 150 0 310 3 1 0 2 4 24 183 94 89 c 0 0 0 0 0 0 0 0 60 56 55 8 165 317 1 311 5 9 1 1 279 30 62 68 g 0 0 0 0 0 0 0 0 68 62 30 279 1 1 9 5 311 1 317 165 8 55 56 60 t 0 0 0 0 0 0 0 0 89 94 183 24 4 2 0 1 3 310 0 150 9 52 108 103

ATAREB1_M0256_1.02_CISBP_shift8 (ATAREB1:M0256_1.02:CISBP) 0.909 0.738 4.868 0.952 0.970 15 3 53 8 10 17.800 4
; oligos_5-8nt_m1 versus ATAREB1_M0256_1.02_CISBP (ATAREB1:M0256_1.02:CISBP); m=4/107; ncol2=13; w=13; offset=0; strand=D; shift=8; score= 17.8; --------cayrACACGTgkt--- ; cor=0.909; Ncor=0.738; logoDP=4.868; NsEucl=0.952; NSW=0.970; rcor=15; rNcor=3; rlogoDP=53; rNsEucl=8; rNSW=10; rank_mean=17.800; match_rank=4 a 0 0 0 0 0 0 0 0 23 31 19 27 70 0 100 0 2 2 22 21 23 0 0 0 c 0 0 0 0 0 0 0 0 31 23 27 12 18 84 0 92 2 2 6 13 23 0 0 0 g 0 0 0 0 0 0 0 0 23 23 19 41 10 0 0 0 94 2 66 29 23 0 0 0 t 0 0 0 0 0 0 0 0 23 23 35 20 2 16 0 8 2 94 6 37 31 0 0 0

ABF2_MA0941.1_JASPAR_shift8 (ABF2:MA0941.1:JASPAR) 0.908 0.738 4.890 0.952 0.969 16 4 52 9 11 18.400 5
; oligos_5-8nt_m1 versus ABF2_MA0941.1_JASPAR (ABF2:MA0941.1:JASPAR); m=5/107; ncol2=13; w=13; offset=0; strand=D; shift=8; score= 18.4; --------cayrACACGTgkt--- ; cor=0.908; Ncor=0.738; logoDP=4.890; NsEucl=0.952; NSW=0.969; rcor=16; rNcor=4; rlogoDP=52; rNsEucl=9; rNSW=11; rank_mean=18.400; match_rank=5 a 0 0 0 0 0 0 0 0 231 308 191 274 699 0 999 0 19 19 218 213 229 0 0 0 c 0 0 0 0 0 0 0 0 308 231 268 120 177 840 0 917 19 19 59 130 229 0 0 0 g 0 0 0 0 0 0 0 0 231 231 191 403 103 0 0 0 942 19 664 287 229 0 0 0 t 0 0 0 0 0 0 0 0 231 231 350 202 21 159 0 82 19 942 59 371 312 0 0 0

BZR1_MA0550.1_JASPAR_rc_shift9 (BZR1:MA0550.1:JASPAR_rc) 0.850 0.743 6.169 0.940 0.949 39 2 32 15 24 22.400 11
; oligos_5-8nt_m1 versus BZR1_MA0550.1_JASPAR_rc (BZR1:MA0550.1:JASPAR_rc); m=11/107; ncol2=14; w=14; offset=1; strand=R; shift=9; score= 22.4; ---------kkbhCACGTGkmkk- ; cor=0.850; Ncor=0.743; logoDP=6.169; NsEucl=0.940; NSW=0.949; rcor=39; rNcor=2; rlogoDP=32; rNsEucl=15; rNSW=24; rank_mean=22.400; match_rank=11 a 0 0 0 0 0 0 0 0 0 33 28 16 72 0 153 0 0 4 0 12 51 24 0 0 c 0 0 0 0 0 0 0 0 0 0 22 43 39 142 0 153 0 0 0 26 52 27 30 0 g 0 0 0 0 0 0 0 0 0 39 61 53 0 5 0 0 147 2 153 66 20 47 60 0 t 0 0 0 0 0 0 0 0 0 81 42 41 42 6 0 0 6 147 0 49 30 55 63 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m1_shift8 (oligos_5-8nt_m1)													; oligos_5-8nt_m1; m=0 (reference); ncol1=16; shift=8; ncol=24; --------wwtGACACGTGTCaww ; Alignment reference a 0 0 0 0 0 0 0 0 88 90 55 29 236 24 291 15 18 11 18 24 39 155 101 103 c 0 0 0 0 0 0 0 0 68 64 57 22 45 263 2 271 8 11 7 8 217 45 58 58 g 0 0 0 0 0 0 0 0 62 61 46 227 7 7 9 9 274 2 267 49 24 58 66 66 t 0 0 0 0 0 0 0 0 95 98 155 35 25 19 11 18 13 289 21 232 33 55 88 86
HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR)	0.949	0.949	6.807	0.965	0.980	7	1	8	1	3	4.000	1	; oligos_5-8nt_m1 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=1/107; ncol2=16; w=16; offset=0; strand=D; shift=8; score= 4; --------wwtGmCACGTGkCaww ; cor=0.949; Ncor=0.949; logoDP=6.807; NsEucl=0.965; NSW=0.980; rcor=7; rNcor=1; rlogoDP=8; rNsEucl=1; rNSW=3; rank_mean=4.000; match_rank=1 a 0 0 0 0 0 0 0 0 103 108 52 9 150 0 310 3 1 0 2 4 24 183 94 89 c 0 0 0 0 0 0 0 0 60 56 55 8 165 317 1 311 5 9 1 1 279 30 62 68 g 0 0 0 0 0 0 0 0 68 62 30 279 1 1 9 5 311 1 317 165 8 55 56 60 t 0 0 0 0 0 0 0 0 89 94 183 24 4 2 0 1 3 310 0 150 9 52 108 103
ATAREB1_M0256_1.02_CISBP_shift8 (ATAREB1:M0256_1.02:CISBP)	0.909	0.738	4.868	0.952	0.970	15	3	53	8	10	17.800	4	; oligos_5-8nt_m1 versus ATAREB1_M0256_1.02_CISBP (ATAREB1:M0256_1.02:CISBP); m=4/107; ncol2=13; w=13; offset=0; strand=D; shift=8; score= 17.8; --------cayrACACGTgkt--- ; cor=0.909; Ncor=0.738; logoDP=4.868; NsEucl=0.952; NSW=0.970; rcor=15; rNcor=3; rlogoDP=53; rNsEucl=8; rNSW=10; rank_mean=17.800; match_rank=4 a 0 0 0 0 0 0 0 0 23 31 19 27 70 0 100 0 2 2 22 21 23 0 0 0 c 0 0 0 0 0 0 0 0 31 23 27 12 18 84 0 92 2 2 6 13 23 0 0 0 g 0 0 0 0 0 0 0 0 23 23 19 41 10 0 0 0 94 2 66 29 23 0 0 0 t 0 0 0 0 0 0 0 0 23 23 35 20 2 16 0 8 2 94 6 37 31 0 0 0
ABF2_MA0941.1_JASPAR_shift8 (ABF2:MA0941.1:JASPAR)	0.908	0.738	4.890	0.952	0.969	16	4	52	9	11	18.400	5	; oligos_5-8nt_m1 versus ABF2_MA0941.1_JASPAR (ABF2:MA0941.1:JASPAR); m=5/107; ncol2=13; w=13; offset=0; strand=D; shift=8; score= 18.4; --------cayrACACGTgkt--- ; cor=0.908; Ncor=0.738; logoDP=4.890; NsEucl=0.952; NSW=0.969; rcor=16; rNcor=4; rlogoDP=52; rNsEucl=9; rNSW=11; rank_mean=18.400; match_rank=5 a 0 0 0 0 0 0 0 0 231 308 191 274 699 0 999 0 19 19 218 213 229 0 0 0 c 0 0 0 0 0 0 0 0 308 231 268 120 177 840 0 917 19 19 59 130 229 0 0 0 g 0 0 0 0 0 0 0 0 231 231 191 403 103 0 0 0 942 19 664 287 229 0 0 0 t 0 0 0 0 0 0 0 0 231 231 350 202 21 159 0 82 19 942 59 371 312 0 0 0
BZR1_MA0550.1_JASPAR_rc_shift9 (BZR1:MA0550.1:JASPAR_rc)	0.850	0.743	6.169	0.940	0.949	39	2	32	15	24	22.400	11	; oligos_5-8nt_m1 versus BZR1_MA0550.1_JASPAR_rc (BZR1:MA0550.1:JASPAR_rc); m=11/107; ncol2=14; w=14; offset=1; strand=R; shift=9; score= 22.4; ---------kkbhCACGTGkmkk- ; cor=0.850; Ncor=0.743; logoDP=6.169; NsEucl=0.940; NSW=0.949; rcor=39; rNcor=2; rlogoDP=32; rNsEucl=15; rNSW=24; rank_mean=22.400; match_rank=11 a 0 0 0 0 0 0 0 0 0 33 28 16 72 0 153 0 0 4 0 12 51 24 0 0 c 0 0 0 0 0 0 0 0 0 0 22 43 39 142 0 153 0 0 0 26 52 27 30 0 g 0 0 0 0 0 0 0 0 0 39 61 53 0 5 0 0 147 2 153 66 20 47 60 0 t 0 0 0 0 0 0 0 0 0 81 42 41 42 6 0 0 6 147 0 49 30 55 63 0