One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/02/compare-matrices_2019-07-02.133714_4HXmRw/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_2019-07-02.133714_4HXmRw/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift3 ; 11 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_shift3 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=3; ncol=21; ---myaAAAACCCwa------ ; Alignment reference a 0 0 0 140 94 247 366 422 420 395 4 8 9 149 207 0 0 0 0 0 0 c 0 0 0 134 141 91 12 11 9 29 437 424 428 88 92 0 0 0 0 0 0 g 0 0 0 64 83 38 31 5 4 3 2 11 4 59 57 0 0 0 0 0 0 t 0 0 0 111 131 73 40 11 16 22 6 6 8 153 93 0 0 0 0 0 0

AT1G76870_MA1367.1_JASPAR_shift2 (AT1G76870:MA1367.1:JASPAR) 0.769 0.659 6.371 0.917 0.916 4 1 4 2 2 2.600 1
; dyads_test_vs_ctrl_m1 versus AT1G76870_MA1367.1_JASPAR (AT1G76870:MA1367.1:JASPAR); m=1/10; ncol2=14; w=12; offset=-1; strand=D; shift=2; score= 2.6; --awmywAAACCrsww----- ; cor=0.769; Ncor=0.659; logoDP=6.371; NsEucl=0.917; NSW=0.916; rcor=4; rNcor=1; rlogoDP=4; rNsEucl=2; rNSW=2; rank_mean=2.600; match_rank=1 a 0 0 209 218 173 87 287 436 418 448 6 0 175 41 177 229 0 0 0 0 0 c 0 0 94 64 127 173 21 5 0 6 450 452 4 150 71 46 0 0 0 0 0 g 0 0 53 59 65 73 3 5 2 0 0 0 257 222 53 35 0 0 0 0 0 t 0 0 100 115 91 123 145 10 36 2 0 4 20 43 155 146 0 0 0 0 0

AT1G72740_MA1353.1_JASPAR_shift4 (AT1G72740:MA1353.1:JASPAR) 0.817 0.562 7.184 0.911 0.913 2 2 3 3 3 2.600 2
; dyads_test_vs_ctrl_m1 versus AT1G72740_MA1353.1_JASPAR (AT1G72740:MA1353.1:JASPAR); m=2/10; ncol2=15; w=11; offset=1; strand=D; shift=4; score= 2.6; ----cctAAACCCTAAwyc-- ; cor=0.817; Ncor=0.562; logoDP=7.184; NsEucl=0.911; NSW=0.913; rcor=2; rNcor=2; rlogoDP=3; rNsEucl=3; rNSW=3; rank_mean=2.600; match_rank=2 a 0 0 0 0 62 69 59 214 282 282 10 0 0 0 289 242 138 9 37 0 0 c 0 0 0 0 154 159 46 3 3 0 281 291 291 0 0 0 41 129 157 0 0 g 0 0 0 0 23 34 51 22 2 9 0 0 0 0 1 49 2 16 27 0 0 t 0 0 0 0 52 29 135 52 4 0 0 0 0 291 1 0 110 137 70 0 0

TBP3.ampDAP_M0621_AthalianaCistrome_rc_shift0 (TBP3.ampDAP:M0621:AthalianaCistrome_rc) 0.793 0.501 0.448 0.920 0.924 3 4 10 1 1 3.800 3
; dyads_test_vs_ctrl_m1 versus TBP3.ampDAP_M0621_AthalianaCistrome_rc (TBP3.ampDAP:M0621:AthalianaCistrome_rc); m=3/10; ncol2=19; w=12; offset=-3; strand=R; shift=0; score= 3.8; maamhhtaARCCCTAAwyy-- ; cor=0.793; Ncor=0.501; logoDP=0.448; NsEucl=0.920; NSW=0.924; rcor=3; rNcor=4; rlogoDP=10; rNsEucl=1; rNSW=1; rank_mean=3.800; match_rank=3 a 126 140 138 102 76 73 50 167 197 186 11 5 0 0 251 231 93 23 51 0 0 c 64 39 30 66 96 83 37 4 2 3 239 237 239 18 3 1 57 71 95 0 0 g 21 48 33 26 19 23 38 35 2 66 1 3 13 5 1 21 9 7 24 0 0 t 44 28 54 61 64 76 130 49 54 0 4 10 3 232 0 2 96 154 85 0 0

At3g13040.DAP_M0399_AthalianaCistrome_shift3 (At3g13040.DAP:M0399:AthalianaCistrome) 0.715 0.536 6.199 0.877 0.865 9 3 5 10 9 7.200 9
; dyads_test_vs_ctrl_m1 versus At3g13040.DAP_M0399_AthalianaCistrome (At3g13040.DAP:M0399:AthalianaCistrome); m=9/10; ncol2=9; w=9; offset=0; strand=D; shift=3; score= 7.2; ---awGAAAACa--------- ; cor=0.715; Ncor=0.536; logoDP=6.199; NsEucl=0.877; NSW=0.865; rcor=9; rNcor=3; rlogoDP=5; rNsEucl=10; rNSW=9; rank_mean=7.200; match_rank=9 a 0 0 0 76 72 0 154 157 150 157 0 88 0 0 0 0 0 0 0 0 0 c 0 0 0 20 10 0 0 0 0 0 157 23 0 0 0 0 0 0 0 0 0 g 0 0 0 24 25 157 3 0 7 0 0 13 0 0 0 0 0 0 0 0 0 t 0 0 0 37 50 0 0 0 0 0 0 33 0 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
dyads_test_vs_ctrl_m1_shift3 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=3; ncol=21; ---myaAAAACCCwa------ ; Alignment reference a 0 0 0 140 94 247 366 422 420 395 4 8 9 149 207 0 0 0 0 0 0 c 0 0 0 134 141 91 12 11 9 29 437 424 428 88 92 0 0 0 0 0 0 g 0 0 0 64 83 38 31 5 4 3 2 11 4 59 57 0 0 0 0 0 0 t 0 0 0 111 131 73 40 11 16 22 6 6 8 153 93 0 0 0 0 0 0
AT1G76870_MA1367.1_JASPAR_shift2 (AT1G76870:MA1367.1:JASPAR)	0.769	0.659	6.371	0.917	0.916	4	1	4	2	2	2.600	1	; dyads_test_vs_ctrl_m1 versus AT1G76870_MA1367.1_JASPAR (AT1G76870:MA1367.1:JASPAR); m=1/10; ncol2=14; w=12; offset=-1; strand=D; shift=2; score= 2.6; --awmywAAACCrsww----- ; cor=0.769; Ncor=0.659; logoDP=6.371; NsEucl=0.917; NSW=0.916; rcor=4; rNcor=1; rlogoDP=4; rNsEucl=2; rNSW=2; rank_mean=2.600; match_rank=1 a 0 0 209 218 173 87 287 436 418 448 6 0 175 41 177 229 0 0 0 0 0 c 0 0 94 64 127 173 21 5 0 6 450 452 4 150 71 46 0 0 0 0 0 g 0 0 53 59 65 73 3 5 2 0 0 0 257 222 53 35 0 0 0 0 0 t 0 0 100 115 91 123 145 10 36 2 0 4 20 43 155 146 0 0 0 0 0
AT1G72740_MA1353.1_JASPAR_shift4 (AT1G72740:MA1353.1:JASPAR)	0.817	0.562	7.184	0.911	0.913	2	2	3	3	3	2.600	2	; dyads_test_vs_ctrl_m1 versus AT1G72740_MA1353.1_JASPAR (AT1G72740:MA1353.1:JASPAR); m=2/10; ncol2=15; w=11; offset=1; strand=D; shift=4; score= 2.6; ----cctAAACCCTAAwyc-- ; cor=0.817; Ncor=0.562; logoDP=7.184; NsEucl=0.911; NSW=0.913; rcor=2; rNcor=2; rlogoDP=3; rNsEucl=3; rNSW=3; rank_mean=2.600; match_rank=2 a 0 0 0 0 62 69 59 214 282 282 10 0 0 0 289 242 138 9 37 0 0 c 0 0 0 0 154 159 46 3 3 0 281 291 291 0 0 0 41 129 157 0 0 g 0 0 0 0 23 34 51 22 2 9 0 0 0 0 1 49 2 16 27 0 0 t 0 0 0 0 52 29 135 52 4 0 0 0 0 291 1 0 110 137 70 0 0
TBP3.ampDAP_M0621_AthalianaCistrome_rc_shift0 (TBP3.ampDAP:M0621:AthalianaCistrome_rc)	0.793	0.501	0.448	0.920	0.924	3	4	10	1	1	3.800	3	; dyads_test_vs_ctrl_m1 versus TBP3.ampDAP_M0621_AthalianaCistrome_rc (TBP3.ampDAP:M0621:AthalianaCistrome_rc); m=3/10; ncol2=19; w=12; offset=-3; strand=R; shift=0; score= 3.8; maamhhtaARCCCTAAwyy-- ; cor=0.793; Ncor=0.501; logoDP=0.448; NsEucl=0.920; NSW=0.924; rcor=3; rNcor=4; rlogoDP=10; rNsEucl=1; rNSW=1; rank_mean=3.800; match_rank=3 a 126 140 138 102 76 73 50 167 197 186 11 5 0 0 251 231 93 23 51 0 0 c 64 39 30 66 96 83 37 4 2 3 239 237 239 18 3 1 57 71 95 0 0 g 21 48 33 26 19 23 38 35 2 66 1 3 13 5 1 21 9 7 24 0 0 t 44 28 54 61 64 76 130 49 54 0 4 10 3 232 0 2 96 154 85 0 0
At3g13040.DAP_M0399_AthalianaCistrome_shift3 (At3g13040.DAP:M0399:AthalianaCistrome)	0.715	0.536	6.199	0.877	0.865	9	3	5	10	9	7.200	9	; dyads_test_vs_ctrl_m1 versus At3g13040.DAP_M0399_AthalianaCistrome (At3g13040.DAP:M0399:AthalianaCistrome); m=9/10; ncol2=9; w=9; offset=0; strand=D; shift=3; score= 7.2; ---awGAAAACa--------- ; cor=0.715; Ncor=0.536; logoDP=6.199; NsEucl=0.877; NSW=0.865; rcor=9; rNcor=3; rlogoDP=5; rNsEucl=10; rNSW=9; rank_mean=7.200; match_rank=9 a 0 0 0 76 72 0 154 157 150 157 0 88 0 0 0 0 0 0 0 0 0 c 0 0 0 20 10 0 0 0 0 0 157 23 0 0 0 0 0 0 0 0 0 g 0 0 0 24 25 157 3 0 7 0 0 13 0 0 0 0 0 0 0 0 0 t 0 0 0 37 50 0 0 0 0 0 0 33 0 0 0 0 0 0 0 0 0