One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/07/compare-matrices_2019-07-07.132738_XZhu42/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_2019-07-07.132738_XZhu42/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift6 ; 72 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

bHLH31_MA1359.1_JASPAR_rc_shift5 (bHLH31:MA1359.1:JASPAR_rc) 0.813 0.774 0.372 0.952 0.954 34 1 67 6 11 23.800 18
; oligos_5-8nt_m1 versus bHLH31_MA1359.1_JASPAR_rc (bHLH31:MA1359.1:JASPAR_rc); m=18/71; ncol2=21; w=20; offset=-1; strand=R; shift=5; score= 23.8; -----gwgwwwsvCACGTGycwcmws ; cor=0.813; Ncor=0.774; logoDP=0.372; NsEucl=0.952; NSW=0.954; rcor=34; rNcor=1; rlogoDP=67; rNsEucl=6; rNSW=11; rank_mean=23.800; match_rank=18 a 0 0 0 0 0 123 160 91 258 190 170 137 165 0 595 0 14 0 0 106 107 232 129 172 234 63 c 0 0 0 0 0 115 83 146 87 97 94 163 180 595 0 547 0 0 0 194 231 83 230 204 54 215 g 0 0 0 0 0 259 101 257 95 121 141 182 167 0 0 0 581 0 595 142 131 116 100 122 44 179 t 0 0 0 0 0 98 251 101 155 187 190 113 83 0 0 48 0 595 0 153 126 164 136 97 263 138

bHLH34.DAP_M0166_AthalianaCistrome_shift5 (bHLH34.DAP:M0166:AthalianaCistrome) 0.861 0.749 6.074 0.959 0.966 13 2 22 1 4 8.400 2
; oligos_5-8nt_m1 versus bHLH34.DAP_M0166_AthalianaCistrome (bHLH34.DAP:M0166:AthalianaCistrome); m=2/71; ncol2=23; w=20; offset=-1; strand=D; shift=5; score= 8.4; -----gtgrwwgrCACGTGycarcwy ; cor=0.861; Ncor=0.749; logoDP=6.074; NsEucl=0.959; NSW=0.966; rcor=13; rNcor=2; rlogoDP=22; rNsEucl=1; rNSW=4; rank_mean=8.400; match_rank=2 a 0 0 0 0 0 118 123 108 154 180 152 140 205 7 549 0 45 13 0 65 89 224 182 139 203 86 c 0 0 0 0 0 68 69 37 124 119 124 72 135 560 6 567 0 68 0 188 308 87 99 213 101 202 g 0 0 0 0 0 329 62 365 162 101 122 242 153 0 9 0 522 2 559 117 85 132 152 105 106 106 t 0 0 0 0 0 52 313 57 127 167 169 113 74 0 3 0 0 484 8 197 85 124 134 110 157 173

PIF3_PIF3_1_Athamap_shift7 (PIF3:PIF3_1:Athamap) 0.805 0.725 7.431 0.941 0.938 43 3 2 12 24 16.800 11
; oligos_5-8nt_m1 versus PIF3_PIF3_1_Athamap (PIF3:PIF3_1:Athamap); m=11/71; ncol2=18; w=18; offset=1; strand=D; shift=7; score= 16.8; -------gkrggmCACGTGrmswCk- ; cor=0.805; Ncor=0.725; logoDP=7.431; NsEucl=0.941; NSW=0.938; rcor=43; rNcor=3; rlogoDP=2; rNsEucl=12; rNSW=24; rank_mean=16.800; match_rank=11 a 0 0 0 0 0 0 0 2 5 11 6 5 11 0 27 0 0 0 0 11 9 3 11 4 4 0 c 0 0 0 0 0 0 0 5 1 2 0 3 11 27 0 27 0 0 0 2 12 9 6 19 2 0 g 0 0 0 0 0 0 0 15 10 12 17 17 5 0 0 0 27 0 27 13 6 13 0 4 9 0 t 0 0 0 0 0 0 0 5 11 2 4 2 0 0 0 0 0 27 0 1 0 2 10 0 12 0

HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR) 0.902 0.721 7.410 0.953 0.965 5 4 4 5 5 4.600 1
; oligos_5-8nt_m1 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=1/71; ncol2=16; w=16; offset=2; strand=D; shift=8; score= 4.6; --------wwtGmCACGTGkCaww-- ; cor=0.902; Ncor=0.721; logoDP=7.410; NsEucl=0.953; NSW=0.965; rcor=5; rNcor=4; rlogoDP=4; rNsEucl=5; rNSW=5; rank_mean=4.600; 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 0 0 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 0 0 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 0 0 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 0 0

oligos_5-8nt_m1_shift6 (oligos_5-8nt_m1)
; oligos_5-8nt_m1; m=0 (reference); ncol1=20; shift=6; ncol=26; ------wwgbgGACACGTGTCcvcww ; Alignment reference a 0 0 0 0 0 0 34 38 22 15 19 6 81 3 98 2 6 4 4 3 11 26 32 25 31 31 c 0 0 0 0 0 0 22 17 17 35 19 7 20 101 5 100 3 4 3 8 86 46 28 47 25 24 g 0 0 0 0 0 0 24 26 48 29 46 87 7 3 4 3 100 5 101 20 7 20 36 17 17 22 t 0 0 0 0 0 0 31 30 24 32 27 11 3 4 4 6 2 98 3 80 7 19 15 22 38 34

Matrix name	cor	Ncor ▴	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
bHLH31_MA1359.1_JASPAR_rc_shift5 (bHLH31:MA1359.1:JASPAR_rc)	0.813	0.774	0.372	0.952	0.954	34	1	67	6	11	23.800	18	; oligos_5-8nt_m1 versus bHLH31_MA1359.1_JASPAR_rc (bHLH31:MA1359.1:JASPAR_rc); m=18/71; ncol2=21; w=20; offset=-1; strand=R; shift=5; score= 23.8; -----gwgwwwsvCACGTGycwcmws ; cor=0.813; Ncor=0.774; logoDP=0.372; NsEucl=0.952; NSW=0.954; rcor=34; rNcor=1; rlogoDP=67; rNsEucl=6; rNSW=11; rank_mean=23.800; match_rank=18 a 0 0 0 0 0 123 160 91 258 190 170 137 165 0 595 0 14 0 0 106 107 232 129 172 234 63 c 0 0 0 0 0 115 83 146 87 97 94 163 180 595 0 547 0 0 0 194 231 83 230 204 54 215 g 0 0 0 0 0 259 101 257 95 121 141 182 167 0 0 0 581 0 595 142 131 116 100 122 44 179 t 0 0 0 0 0 98 251 101 155 187 190 113 83 0 0 48 0 595 0 153 126 164 136 97 263 138
bHLH34.DAP_M0166_AthalianaCistrome_shift5 (bHLH34.DAP:M0166:AthalianaCistrome)	0.861	0.749	6.074	0.959	0.966	13	2	22	1	4	8.400	2	; oligos_5-8nt_m1 versus bHLH34.DAP_M0166_AthalianaCistrome (bHLH34.DAP:M0166:AthalianaCistrome); m=2/71; ncol2=23; w=20; offset=-1; strand=D; shift=5; score= 8.4; -----gtgrwwgrCACGTGycarcwy ; cor=0.861; Ncor=0.749; logoDP=6.074; NsEucl=0.959; NSW=0.966; rcor=13; rNcor=2; rlogoDP=22; rNsEucl=1; rNSW=4; rank_mean=8.400; match_rank=2 a 0 0 0 0 0 118 123 108 154 180 152 140 205 7 549 0 45 13 0 65 89 224 182 139 203 86 c 0 0 0 0 0 68 69 37 124 119 124 72 135 560 6 567 0 68 0 188 308 87 99 213 101 202 g 0 0 0 0 0 329 62 365 162 101 122 242 153 0 9 0 522 2 559 117 85 132 152 105 106 106 t 0 0 0 0 0 52 313 57 127 167 169 113 74 0 3 0 0 484 8 197 85 124 134 110 157 173
PIF3_PIF3_1_Athamap_shift7 (PIF3:PIF3_1:Athamap)	0.805	0.725	7.431	0.941	0.938	43	3	2	12	24	16.800	11	; oligos_5-8nt_m1 versus PIF3_PIF3_1_Athamap (PIF3:PIF3_1:Athamap); m=11/71; ncol2=18; w=18; offset=1; strand=D; shift=7; score= 16.8; -------gkrggmCACGTGrmswCk- ; cor=0.805; Ncor=0.725; logoDP=7.431; NsEucl=0.941; NSW=0.938; rcor=43; rNcor=3; rlogoDP=2; rNsEucl=12; rNSW=24; rank_mean=16.800; match_rank=11 a 0 0 0 0 0 0 0 2 5 11 6 5 11 0 27 0 0 0 0 11 9 3 11 4 4 0 c 0 0 0 0 0 0 0 5 1 2 0 3 11 27 0 27 0 0 0 2 12 9 6 19 2 0 g 0 0 0 0 0 0 0 15 10 12 17 17 5 0 0 0 27 0 27 13 6 13 0 4 9 0 t 0 0 0 0 0 0 0 5 11 2 4 2 0 0 0 0 0 27 0 1 0 2 10 0 12 0
HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR)	0.902	0.721	7.410	0.953	0.965	5	4	4	5	5	4.600	1	; oligos_5-8nt_m1 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=1/71; ncol2=16; w=16; offset=2; strand=D; shift=8; score= 4.6; --------wwtGmCACGTGkCaww-- ; cor=0.902; Ncor=0.721; logoDP=7.410; NsEucl=0.953; NSW=0.965; rcor=5; rNcor=4; rlogoDP=4; rNsEucl=5; rNSW=5; rank_mean=4.600; 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 0 0 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 0 0 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 0 0 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 0 0
oligos_5-8nt_m1_shift6 (oligos_5-8nt_m1)													; oligos_5-8nt_m1; m=0 (reference); ncol1=20; shift=6; ncol=26; ------wwgbgGACACGTGTCcvcww ; Alignment reference a 0 0 0 0 0 0 34 38 22 15 19 6 81 3 98 2 6 4 4 3 11 26 32 25 31 31 c 0 0 0 0 0 0 22 17 17 35 19 7 20 101 5 100 3 4 3 8 86 46 28 47 25 24 g 0 0 0 0 0 0 24 26 48 29 46 87 7 3 4 3 100 5 101 20 7 20 36 17 17 22 t 0 0 0 0 0 0 31 30 24 32 27 11 3 4 4 6 2 98 3 80 7 19 15 22 38 34