One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/02/compare-matrices_2019-07-02.154732_THaihH/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_2019-07-02.154732_THaihH/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift5 ; 35 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_shift5 (oligos_5-8nt_m1)
; oligos_5-8nt_m1; m=0 (reference); ncol1=22; shift=5; ncol=27; -----wraaccgACACGTGTcggtthw ; Alignment reference a 0 0 0 0 0 39 51 66 69 27 16 24 111 5 122 7 12 8 3 10 17 26 18 30 31 36 40 c 0 0 0 0 0 29 19 16 25 69 89 13 20 132 6 120 3 7 2 2 87 9 27 19 28 37 35 g 0 0 0 0 0 34 37 29 19 27 12 87 2 2 7 3 120 4 132 20 13 91 72 24 16 19 29 t 0 0 0 0 0 40 35 31 29 19 25 18 9 3 7 12 7 123 5 110 25 16 25 69 67 50 38

HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR) 0.834 0.607 6.663 0.939 0.941 10 3 3 9 10 7.000 1
; oligos_5-8nt_m1 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=1/34; ncol2=16; w=16; offset=3; strand=D; shift=8; score= 7; --------wwtGmCACGTGkCaww--- ; cor=0.834; Ncor=0.607; logoDP=6.663; NsEucl=0.939; NSW=0.941; rcor=10; rNcor=3; rlogoDP=3; rNsEucl=9; rNSW=10; rank_mean=7.000; 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 0 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 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 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 0

bHLH34.DAP_M0166_AthalianaCistrome_shift5 (bHLH34.DAP:M0166:AthalianaCistrome) 0.775 0.741 5.693 0.952 0.948 20 1 13 1 7 8.400 3
; oligos_5-8nt_m1 versus bHLH34.DAP_M0166_AthalianaCistrome (bHLH34.DAP:M0166:AthalianaCistrome); m=3/34; ncol2=23; w=22; offset=0; strand=D; shift=5; score= 8.4; -----gtgrwwgrCACGTGycarcwyg ; cor=0.775; Ncor=0.741; logoDP=5.693; NsEucl=0.952; NSW=0.948; rcor=20; rNcor=1; rlogoDP=13; rNsEucl=1; rNSW=7; rank_mean=8.400; match_rank=3 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 86 136 c 0 0 0 0 0 68 69 37 124 119 124 72 135 560 6 567 0 68 0 188 308 87 99 213 101 202 105 g 0 0 0 0 0 329 62 365 162 101 122 242 153 0 9 0 522 2 559 117 85 132 152 105 106 106 211 t 0 0 0 0 0 52 313 57 127 167 169 113 74 0 3 0 0 484 8 197 85 124 134 110 157 173 115

bHLH31_MA1359.1_JASPAR_rc_shift5 (bHLH31:MA1359.1:JASPAR_rc) 0.753 0.719 0.383 0.947 0.941 22 2 30 2 11 13.400 12
; oligos_5-8nt_m1 versus bHLH31_MA1359.1_JASPAR_rc (bHLH31:MA1359.1:JASPAR_rc); m=12/34; ncol2=21; w=21; offset=0; strand=R; shift=5; score= 13.4; -----gwgwwwsvCACGTGycwcmws- ; cor=0.753; Ncor=0.719; logoDP=0.383; NsEucl=0.947; NSW=0.941; rcor=22; rNcor=2; rlogoDP=30; rNsEucl=2; rNSW=11; rank_mean=13.400; match_rank=12 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 0 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 0 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 0 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 0

ABF2.DAP_M0217_AthalianaCistrome_rc_shift9 (ABF2.DAP:M0217:AthalianaCistrome_rc) 0.718 0.588 0.396 0.930 0.912 30 4 29 17 25 21.000 21
; oligos_5-8nt_m1 versus ABF2.DAP_M0217_AthalianaCistrome_rc (ABF2.DAP:M0217:AthalianaCistrome_rc); m=21/34; ncol2=18; w=18; offset=4; strand=R; shift=9; score= 21; ---------wggwsACGTGKCAwwwth ; cor=0.718; Ncor=0.588; logoDP=0.396; NsEucl=0.930; NSW=0.912; rcor=30; rNcor=4; rlogoDP=29; rNsEucl=17; rNSW=25; rank_mean=21.000; match_rank=21 a 0 0 0 0 0 0 0 0 0 180 56 143 241 0 595 0 0 1 0 0 27 432 163 193 209 141 152 c 0 0 0 0 0 0 0 0 0 40 29 104 92 323 0 595 0 0 0 0 567 54 110 80 78 96 157 g 0 0 0 0 0 0 0 0 0 94 380 305 0 252 0 0 595 0 595 421 0 84 138 85 43 80 79 t 0 0 0 0 0 0 0 0 0 281 130 43 262 20 0 0 0 594 0 174 1 25 184 237 265 278 207

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m1_shift5 (oligos_5-8nt_m1)													; oligos_5-8nt_m1; m=0 (reference); ncol1=22; shift=5; ncol=27; -----wraaccgACACGTGTcggtthw ; Alignment reference a 0 0 0 0 0 39 51 66 69 27 16 24 111 5 122 7 12 8 3 10 17 26 18 30 31 36 40 c 0 0 0 0 0 29 19 16 25 69 89 13 20 132 6 120 3 7 2 2 87 9 27 19 28 37 35 g 0 0 0 0 0 34 37 29 19 27 12 87 2 2 7 3 120 4 132 20 13 91 72 24 16 19 29 t 0 0 0 0 0 40 35 31 29 19 25 18 9 3 7 12 7 123 5 110 25 16 25 69 67 50 38
HY5_MA0551.1_JASPAR_shift8 (HY5:MA0551.1:JASPAR)	0.834	0.607	6.663	0.939	0.941	10	3	3	9	10	7.000	1	; oligos_5-8nt_m1 versus HY5_MA0551.1_JASPAR (HY5:MA0551.1:JASPAR); m=1/34; ncol2=16; w=16; offset=3; strand=D; shift=8; score= 7; --------wwtGmCACGTGkCaww--- ; cor=0.834; Ncor=0.607; logoDP=6.663; NsEucl=0.939; NSW=0.941; rcor=10; rNcor=3; rlogoDP=3; rNsEucl=9; rNSW=10; rank_mean=7.000; 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 0 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 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 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 0
bHLH34.DAP_M0166_AthalianaCistrome_shift5 (bHLH34.DAP:M0166:AthalianaCistrome)	0.775	0.741	5.693	0.952	0.948	20	1	13	1	7	8.400	3	; oligos_5-8nt_m1 versus bHLH34.DAP_M0166_AthalianaCistrome (bHLH34.DAP:M0166:AthalianaCistrome); m=3/34; ncol2=23; w=22; offset=0; strand=D; shift=5; score= 8.4; -----gtgrwwgrCACGTGycarcwyg ; cor=0.775; Ncor=0.741; logoDP=5.693; NsEucl=0.952; NSW=0.948; rcor=20; rNcor=1; rlogoDP=13; rNsEucl=1; rNSW=7; rank_mean=8.400; match_rank=3 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 86 136 c 0 0 0 0 0 68 69 37 124 119 124 72 135 560 6 567 0 68 0 188 308 87 99 213 101 202 105 g 0 0 0 0 0 329 62 365 162 101 122 242 153 0 9 0 522 2 559 117 85 132 152 105 106 106 211 t 0 0 0 0 0 52 313 57 127 167 169 113 74 0 3 0 0 484 8 197 85 124 134 110 157 173 115
bHLH31_MA1359.1_JASPAR_rc_shift5 (bHLH31:MA1359.1:JASPAR_rc)	0.753	0.719	0.383	0.947	0.941	22	2	30	2	11	13.400	12	; oligos_5-8nt_m1 versus bHLH31_MA1359.1_JASPAR_rc (bHLH31:MA1359.1:JASPAR_rc); m=12/34; ncol2=21; w=21; offset=0; strand=R; shift=5; score= 13.4; -----gwgwwwsvCACGTGycwcmws- ; cor=0.753; Ncor=0.719; logoDP=0.383; NsEucl=0.947; NSW=0.941; rcor=22; rNcor=2; rlogoDP=30; rNsEucl=2; rNSW=11; rank_mean=13.400; match_rank=12 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 0 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 0 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 0 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 0
ABF2.DAP_M0217_AthalianaCistrome_rc_shift9 (ABF2.DAP:M0217:AthalianaCistrome_rc)	0.718	0.588	0.396	0.930	0.912	30	4	29	17	25	21.000	21	; oligos_5-8nt_m1 versus ABF2.DAP_M0217_AthalianaCistrome_rc (ABF2.DAP:M0217:AthalianaCistrome_rc); m=21/34; ncol2=18; w=18; offset=4; strand=R; shift=9; score= 21; ---------wggwsACGTGKCAwwwth ; cor=0.718; Ncor=0.588; logoDP=0.396; NsEucl=0.930; NSW=0.912; rcor=30; rNcor=4; rlogoDP=29; rNsEucl=17; rNSW=25; rank_mean=21.000; match_rank=21 a 0 0 0 0 0 0 0 0 0 180 56 143 241 0 595 0 0 1 0 0 27 432 163 193 209 141 152 c 0 0 0 0 0 0 0 0 0 40 29 104 92 323 0 595 0 0 0 0 567 54 110 80 78 96 157 g 0 0 0 0 0 0 0 0 0 94 380 305 0 252 0 0 595 0 595 421 0 84 138 85 43 80 79 t 0 0 0 0 0 0 0 0 0 281 130 43 262 20 0 0 0 594 0 174 1 25 184 237 265 278 207