One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/03/compare-matrices_2019-07-03.170111_NhmHV0/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_2019-07-03.170111_NhmHV0/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift8 ; 148 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_shift8 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=8; ncol=29; --------wwgAAAAGTCaaaww------ ; Alignment reference a 0 0 0 0 0 0 0 0 134 132 72 279 365 360 367 19 20 21 222 215 214 128 131 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 59 46 24 44 9 6 7 5 7 342 52 35 49 69 62 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 70 69 246 24 7 7 4 345 7 11 37 55 53 88 87 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 127 143 48 43 9 17 12 21 356 16 79 85 74 105 110 0 0 0 0 0 0

WRKY40.ampDAP_M0835_AthalianaCistrome_shift9 (WRKY40.ampDAP:M0835:AthalianaCistrome) 0.860 0.745 5.440 0.936 0.947 15 4 35 4 8 13.200 3
; dyads_test_vs_ctrl_m1 versus WRKY40.ampDAP_M0835_AthalianaCistrome (WRKY40.ampDAP:M0835:AthalianaCistrome); m=3/147; ncol2=13; w=13; offset=1; strand=D; shift=9; score= 13.2; ---------raaAAAGTCAAmr------- ; cor=0.860; Ncor=0.745; logoDP=5.440; NsEucl=0.936; NSW=0.947; rcor=15; rNcor=4; rlogoDP=35; rNsEucl=4; rNSW=8; rank_mean=13.200; match_rank=3 a 0 0 0 0 0 0 0 0 0 190 231 291 385 421 477 0 0 0 561 561 150 196 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 105 83 111 84 43 0 0 5 561 0 0 281 75 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 146 126 87 47 12 84 561 0 0 0 0 82 241 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 120 121 72 45 85 0 0 556 0 0 0 48 49 0 0 0 0 0 0 0

WRKY50_MA1317.1_JASPAR_rc_shift9 (WRKY50:MA1317.1:JASPAR_rc) 0.910 0.789 2.775 0.945 0.960 3 2 83 2 2 18.400 6
; dyads_test_vs_ctrl_m1 versus WRKY50_MA1317.1_JASPAR_rc (WRKY50:MA1317.1:JASPAR_rc); m=6/147; ncol2=13; w=13; offset=1; strand=R; shift=9; score= 18.4; ---------waAAAAGTCAAmr------- ; cor=0.910; Ncor=0.789; logoDP=2.775; NsEucl=0.945; NSW=0.960; rcor=3; rNcor=2; rlogoDP=83; rNsEucl=2; rNSW=2; rank_mean=18.400; match_rank=6 a 0 0 0 0 0 0 0 0 0 215 274 406 502 511 543 0 0 0 565 559 239 163 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 87 90 48 14 4 1 0 1 568 0 2 216 88 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 124 88 63 23 10 22 568 0 0 0 1 56 213 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 142 116 51 29 43 2 0 567 0 3 6 57 104 0 0 0 0 0 0 0

WRKY40.DAP_M0812_AthalianaCistrome_rc_shift9 (WRKY40.DAP:M0812:AthalianaCistrome_rc) 0.852 0.745 2.508 0.940 0.949 22 3 92 3 6 25.200 10
; dyads_test_vs_ctrl_m1 versus WRKY40.DAP_M0812_AthalianaCistrome_rc (WRKY40.DAP:M0812:AthalianaCistrome_rc); m=10/147; ncol2=15; w=14; offset=1; strand=R; shift=9; score= 25.2; ---------raaaAAGTCAAmrwh----- ; cor=0.852; Ncor=0.745; logoDP=2.508; NsEucl=0.940; NSW=0.949; rcor=22; rNcor=3; rlogoDP=92; rNsEucl=3; rNSW=6; rank_mean=25.200; match_rank=10 a 0 0 0 0 0 0 0 0 0 190 249 315 399 433 475 0 0 1 600 594 161 171 165 166 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 98 82 129 97 40 0 0 3 599 0 0 279 77 125 173 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 163 131 90 37 19 125 600 0 0 0 0 89 291 136 69 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 149 138 66 67 108 0 0 597 0 0 6 71 61 174 192 0 0 0 0 0

WRKY43.ampDAP_M0828_AthalianaCistrome_shift8 (WRKY43.ampDAP:M0828:AthalianaCistrome) 0.792 0.792 5.405 0.930 0.927 58 1 37 16 52 32.800 15
; dyads_test_vs_ctrl_m1 versus WRKY43.ampDAP_M0828_AthalianaCistrome (WRKY43.ampDAP:M0828:AthalianaCistrome); m=15/147; ncol2=15; w=15; offset=0; strand=D; shift=8; score= 32.8; --------waaaAAAGTCAACGm------ ; cor=0.792; Ncor=0.792; logoDP=5.405; NsEucl=0.930; NSW=0.927; rcor=58; rNcor=1; rlogoDP=37; rNsEucl=16; rNSW=52; rank_mean=32.800; match_rank=15 a 0 0 0 0 0 0 0 0 242 225 251 321 423 423 467 0 0 0 589 589 71 83 188 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 119 104 110 89 33 41 0 0 0 589 0 0 498 42 160 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 75 125 115 88 42 21 122 589 0 0 0 0 0 419 118 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 153 135 113 91 91 104 0 0 589 0 0 0 20 45 123 0 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m1_shift8 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=15; shift=8; ncol=29; --------wwgAAAAGTCaaaww------ ; Alignment reference a 0 0 0 0 0 0 0 0 134 132 72 279 365 360 367 19 20 21 222 215 214 128 131 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 59 46 24 44 9 6 7 5 7 342 52 35 49 69 62 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 70 69 246 24 7 7 4 345 7 11 37 55 53 88 87 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 127 143 48 43 9 17 12 21 356 16 79 85 74 105 110 0 0 0 0 0 0
WRKY40.ampDAP_M0835_AthalianaCistrome_shift9 (WRKY40.ampDAP:M0835:AthalianaCistrome)	0.860	0.745	5.440	0.936	0.947	15	4	35	4	8	13.200	3	; dyads_test_vs_ctrl_m1 versus WRKY40.ampDAP_M0835_AthalianaCistrome (WRKY40.ampDAP:M0835:AthalianaCistrome); m=3/147; ncol2=13; w=13; offset=1; strand=D; shift=9; score= 13.2; ---------raaAAAGTCAAmr------- ; cor=0.860; Ncor=0.745; logoDP=5.440; NsEucl=0.936; NSW=0.947; rcor=15; rNcor=4; rlogoDP=35; rNsEucl=4; rNSW=8; rank_mean=13.200; match_rank=3 a 0 0 0 0 0 0 0 0 0 190 231 291 385 421 477 0 0 0 561 561 150 196 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 105 83 111 84 43 0 0 5 561 0 0 281 75 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 146 126 87 47 12 84 561 0 0 0 0 82 241 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 120 121 72 45 85 0 0 556 0 0 0 48 49 0 0 0 0 0 0 0
WRKY50_MA1317.1_JASPAR_rc_shift9 (WRKY50:MA1317.1:JASPAR_rc)	0.910	0.789	2.775	0.945	0.960	3	2	83	2	2	18.400	6	; dyads_test_vs_ctrl_m1 versus WRKY50_MA1317.1_JASPAR_rc (WRKY50:MA1317.1:JASPAR_rc); m=6/147; ncol2=13; w=13; offset=1; strand=R; shift=9; score= 18.4; ---------waAAAAGTCAAmr------- ; cor=0.910; Ncor=0.789; logoDP=2.775; NsEucl=0.945; NSW=0.960; rcor=3; rNcor=2; rlogoDP=83; rNsEucl=2; rNSW=2; rank_mean=18.400; match_rank=6 a 0 0 0 0 0 0 0 0 0 215 274 406 502 511 543 0 0 0 565 559 239 163 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 87 90 48 14 4 1 0 1 568 0 2 216 88 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 124 88 63 23 10 22 568 0 0 0 1 56 213 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 142 116 51 29 43 2 0 567 0 3 6 57 104 0 0 0 0 0 0 0
WRKY40.DAP_M0812_AthalianaCistrome_rc_shift9 (WRKY40.DAP:M0812:AthalianaCistrome_rc)	0.852	0.745	2.508	0.940	0.949	22	3	92	3	6	25.200	10	; dyads_test_vs_ctrl_m1 versus WRKY40.DAP_M0812_AthalianaCistrome_rc (WRKY40.DAP:M0812:AthalianaCistrome_rc); m=10/147; ncol2=15; w=14; offset=1; strand=R; shift=9; score= 25.2; ---------raaaAAGTCAAmrwh----- ; cor=0.852; Ncor=0.745; logoDP=2.508; NsEucl=0.940; NSW=0.949; rcor=22; rNcor=3; rlogoDP=92; rNsEucl=3; rNSW=6; rank_mean=25.200; match_rank=10 a 0 0 0 0 0 0 0 0 0 190 249 315 399 433 475 0 0 1 600 594 161 171 165 166 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 98 82 129 97 40 0 0 3 599 0 0 279 77 125 173 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 163 131 90 37 19 125 600 0 0 0 0 89 291 136 69 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 149 138 66 67 108 0 0 597 0 0 6 71 61 174 192 0 0 0 0 0
WRKY43.ampDAP_M0828_AthalianaCistrome_shift8 (WRKY43.ampDAP:M0828:AthalianaCistrome)	0.792	0.792	5.405	0.930	0.927	58	1	37	16	52	32.800	15	; dyads_test_vs_ctrl_m1 versus WRKY43.ampDAP_M0828_AthalianaCistrome (WRKY43.ampDAP:M0828:AthalianaCistrome); m=15/147; ncol2=15; w=15; offset=0; strand=D; shift=8; score= 32.8; --------waaaAAAGTCAACGm------ ; cor=0.792; Ncor=0.792; logoDP=5.405; NsEucl=0.930; NSW=0.927; rcor=58; rNcor=1; rlogoDP=37; rNsEucl=16; rNSW=52; rank_mean=32.800; match_rank=15 a 0 0 0 0 0 0 0 0 242 225 251 321 423 423 467 0 0 0 589 589 71 83 188 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 119 104 110 89 33 41 0 0 0 589 0 0 498 42 160 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 75 125 115 88 42 21 122 589 0 0 0 0 0 419 118 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 153 135 113 91 91 104 0 0 589 0 0 0 20 45 123 0 0 0 0 0 0