One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/07/compare-matrices_2019-07-07.121326_OeEJMP/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/2019/07/07/compare-matrices_2019-07-07.121326_OeEJMP/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m2_shift8 ; 116 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_m2_shift8 (dyads_test_vs_ctrl_m2)
; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=16; shift=8; ncol=24; --------dhtGmCACGTGkCarh ; Alignment reference a 0 0 0 0 0 0 0 0 78 65 44 28 167 9 244 6 11 8 8 14 27 107 74 68 c 0 0 0 0 0 0 0 0 44 67 56 16 67 219 1 229 4 9 5 11 186 52 53 65 g 0 0 0 0 0 0 0 0 68 50 48 183 8 10 8 4 234 0 237 156 14 54 69 53 t 0 0 0 0 0 0 0 0 64 72 106 27 12 16 1 15 5 237 4 73 27 41 58 68

HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR) 0.973 0.973 7.904 0.973 0.989 6 1 15 1 4 5.400 1
; dyads_test_vs_ctrl_m2 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=1/115; ncol2=16; w=16; offset=0; strand=D; shift=8; score= 5.4; --------wwtGmCACGTGkCaww ; cor=0.973; Ncor=0.973; logoDP=7.904; NsEucl=0.973; NSW=0.989; rcor=6; rNcor=1; rlogoDP=15; rNsEucl=1; rNSW=4; rank_mean=5.400; 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

ABI5.DAP_M0201_AthalianaCistrome_shift6 (ABI5.DAP:M0201:AthalianaCistrome) 0.872 0.775 7.904 0.947 0.955 54 4 16 25 34 26.600 16
; dyads_test_vs_ctrl_m2 versus ABI5.DAP_M0201_AthalianaCistrome (ABI5.DAP:M0201:AthalianaCistrome); m=16/115; ncol2=18; w=16; offset=-2; strand=D; shift=6; score= 26.6; ------wdrwgrwsACGTGKCarw ; cor=0.872; Ncor=0.775; logoDP=7.904; NsEucl=0.947; NSW=0.955; rcor=54; rNcor=4; rlogoDP=16; rNsEucl=25; rNSW=34; rank_mean=26.600; match_rank=16 a 0 0 0 0 0 0 241 217 224 161 44 157 198 0 595 0 0 0 0 0 27 394 151 190 c 0 0 0 0 0 0 71 59 80 39 19 119 92 289 0 595 0 0 0 0 568 50 124 117 g 0 0 0 0 0 0 131 167 158 98 400 296 0 294 0 0 595 0 595 446 0 123 174 87 t 0 0 0 0 0 0 152 152 133 297 132 23 305 12 0 0 0 595 0 149 0 28 146 201

BZR1_MA0550.1_JASPAR_rc_shift9 (BZR1:MA0550.1:JASPAR_rc) 0.888 0.777 7.182 0.948 0.962 46 3 40 24 28 28.200 19
; dyads_test_vs_ctrl_m2 versus BZR1_MA0550.1_JASPAR_rc (BZR1:MA0550.1:JASPAR_rc); m=19/115; ncol2=14; w=14; offset=1; strand=R; shift=9; score= 28.2; ---------kkbhCACGTGkmkk- ; cor=0.888; Ncor=0.777; logoDP=7.182; NsEucl=0.948; NSW=0.962; rcor=46; rNcor=3; rlogoDP=40; rNsEucl=24; rNSW=28; rank_mean=28.200; match_rank=19 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

PIF3_PIF3_2_Athamap_shift8 (PIF3:PIF3_2:Athamap) 0.830 0.782 8.481 0.938 0.939 88 2 2 34 59 37.000 28
; dyads_test_vs_ctrl_m2 versus PIF3_PIF3_2_Athamap (PIF3:PIF3_2:Athamap); m=28/115; ncol2=17; w=16; offset=0; strand=D; shift=8; score= 37; --------rdrvCCACGTGGvmvs ; cor=0.830; Ncor=0.782; logoDP=8.481; NsEucl=0.938; NSW=0.939; rcor=88; rNcor=2; rlogoDP=2; rNsEucl=34; rNSW=59; rank_mean=37.000; match_rank=28 a 0 0 0 0 0 0 0 0 15 9 10 8 1 0 32 0 0 0 0 0 9 15 11 7 c 0 0 0 0 0 0 0 0 2 4 2 11 26 32 0 32 0 0 0 0 10 15 13 8 g 0 0 0 0 0 0 0 0 9 10 13 13 5 0 0 0 32 0 32 32 11 0 8 11 t 0 0 0 0 0 0 0 0 6 9 7 0 0 0 0 0 0 32 0 0 2 2 0 6

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m2_shift8 (dyads_test_vs_ctrl_m2)													; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=16; shift=8; ncol=24; --------dhtGmCACGTGkCarh ; Alignment reference a 0 0 0 0 0 0 0 0 78 65 44 28 167 9 244 6 11 8 8 14 27 107 74 68 c 0 0 0 0 0 0 0 0 44 67 56 16 67 219 1 229 4 9 5 11 186 52 53 65 g 0 0 0 0 0 0 0 0 68 50 48 183 8 10 8 4 234 0 237 156 14 54 69 53 t 0 0 0 0 0 0 0 0 64 72 106 27 12 16 1 15 5 237 4 73 27 41 58 68
HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR)	0.973	0.973	7.904	0.973	0.989	6	1	15	1	4	5.400	1	; dyads_test_vs_ctrl_m2 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=1/115; ncol2=16; w=16; offset=0; strand=D; shift=8; score= 5.4; --------wwtGmCACGTGkCaww ; cor=0.973; Ncor=0.973; logoDP=7.904; NsEucl=0.973; NSW=0.989; rcor=6; rNcor=1; rlogoDP=15; rNsEucl=1; rNSW=4; rank_mean=5.400; 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
ABI5.DAP_M0201_AthalianaCistrome_shift6 (ABI5.DAP:M0201:AthalianaCistrome)	0.872	0.775	7.904	0.947	0.955	54	4	16	25	34	26.600	16	; dyads_test_vs_ctrl_m2 versus ABI5.DAP_M0201_AthalianaCistrome (ABI5.DAP:M0201:AthalianaCistrome); m=16/115; ncol2=18; w=16; offset=-2; strand=D; shift=6; score= 26.6; ------wdrwgrwsACGTGKCarw ; cor=0.872; Ncor=0.775; logoDP=7.904; NsEucl=0.947; NSW=0.955; rcor=54; rNcor=4; rlogoDP=16; rNsEucl=25; rNSW=34; rank_mean=26.600; match_rank=16 a 0 0 0 0 0 0 241 217 224 161 44 157 198 0 595 0 0 0 0 0 27 394 151 190 c 0 0 0 0 0 0 71 59 80 39 19 119 92 289 0 595 0 0 0 0 568 50 124 117 g 0 0 0 0 0 0 131 167 158 98 400 296 0 294 0 0 595 0 595 446 0 123 174 87 t 0 0 0 0 0 0 152 152 133 297 132 23 305 12 0 0 0 595 0 149 0 28 146 201
BZR1_MA0550.1_JASPAR_rc_shift9 (BZR1:MA0550.1:JASPAR_rc)	0.888	0.777	7.182	0.948	0.962	46	3	40	24	28	28.200	19	; dyads_test_vs_ctrl_m2 versus BZR1_MA0550.1_JASPAR_rc (BZR1:MA0550.1:JASPAR_rc); m=19/115; ncol2=14; w=14; offset=1; strand=R; shift=9; score= 28.2; ---------kkbhCACGTGkmkk- ; cor=0.888; Ncor=0.777; logoDP=7.182; NsEucl=0.948; NSW=0.962; rcor=46; rNcor=3; rlogoDP=40; rNsEucl=24; rNSW=28; rank_mean=28.200; match_rank=19 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
PIF3_PIF3_2_Athamap_shift8 (PIF3:PIF3_2:Athamap)	0.830	0.782	8.481	0.938	0.939	88	2	2	34	59	37.000	28	; dyads_test_vs_ctrl_m2 versus PIF3_PIF3_2_Athamap (PIF3:PIF3_2:Athamap); m=28/115; ncol2=17; w=16; offset=0; strand=D; shift=8; score= 37; --------rdrvCCACGTGGvmvs ; cor=0.830; Ncor=0.782; logoDP=8.481; NsEucl=0.938; NSW=0.939; rcor=88; rNcor=2; rlogoDP=2; rNsEucl=34; rNSW=59; rank_mean=37.000; match_rank=28 a 0 0 0 0 0 0 0 0 15 9 10 8 1 0 32 0 0 0 0 0 9 15 11 7 c 0 0 0 0 0 0 0 0 2 4 2 11 26 32 0 32 0 0 0 0 10 15 13 8 g 0 0 0 0 0 0 0 0 9 10 13 13 5 0 0 0 32 0 32 32 11 0 8 11 t 0 0 0 0 0 0 0 0 6 9 7 0 0 0 0 0 0 32 0 0 2 2 0 6