One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/apache/2019/10/25/compare-matrices_2019-10-25.142850_sxFwVa/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/apache/2019/10/25/compare-matrices_2019-10-25.142850_sxFwVa/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m2_shift3 ; 7 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_m2_shift3 (oligos_5-8nt_m2)
; oligos_5-8nt_m2; m=0 (reference); ncol1=21; shift=3; ncol=24; ---bbcAAAACCCTAdtkmhcvwy ; Alignment reference a 0 0 0 1 1 2 14 16 15 16 0 0 0 1 12 4 3 3 4 4 1 4 7 3 c 0 0 0 4 6 9 0 0 0 0 14 16 16 1 2 2 3 3 10 4 9 4 3 5 g 0 0 0 5 4 2 2 0 1 0 1 0 0 0 1 6 1 6 1 2 3 5 1 3 t 0 0 0 6 5 3 0 0 0 0 1 0 0 14 1 4 9 4 1 6 3 3 5 5

AT1G72740_MA1353.1_JASPAR_shift4 (AT1G72740:MA1353.1:JASPAR) 0.849 0.607 10.200 0.935 0.936 3 2 1 2 3 2.200 1
; oligos_5-8nt_m2 versus AT1G72740_MA1353.1_JASPAR (AT1G72740:MA1353.1:JASPAR); m=1/6; ncol2=15; w=15; offset=1; strand=D; shift=4; score= 2.2; ----cctAAACCCTAAwyc----- ; cor=0.849; Ncor=0.607; logoDP=10.200; NsEucl=0.935; NSW=0.936; rcor=3; rNcor=2; rlogoDP=1; rNsEucl=2; rNSW=3; rank_mean=2.200; match_rank=1 a 0 0 0 0 62 69 59 214 282 282 10 0 0 0 289 242 138 9 37 0 0 0 0 0 c 0 0 0 0 154 159 46 3 3 0 281 291 291 0 0 0 41 129 157 0 0 0 0 0 g 0 0 0 0 23 34 51 22 2 9 0 0 0 0 1 49 2 16 27 0 0 0 0 0 t 0 0 0 0 52 29 135 52 4 0 0 0 0 291 1 0 110 137 70 0 0 0 0 0

AT1G72740.ampDAP_M0588_AthalianaCistrome_rc_shift5 (AT1G72740.ampDAP:M0588:AthalianaCistrome_rc) 0.841 0.695 0.622 0.948 0.948 4 1 6 1 1 2.600 2
; oligos_5-8nt_m2 versus AT1G72740.ampDAP_M0588_AthalianaCistrome_rc (AT1G72740.ampDAP:M0588:AthalianaCistrome_rc); m=2/6; ncol2=21; w=19; offset=2; strand=R; shift=5; score= 2.6; -----mwAAACCCTAAwyyywwww ; cor=0.841; Ncor=0.695; logoDP=0.622; NsEucl=0.948; NSW=0.948; rcor=4; rNcor=1; rlogoDP=6; rNsEucl=1; rNSW=1; rank_mean=2.600; match_rank=2 a 0 0 0 0 0 181 161 410 562 558 37 0 1 0 592 454 216 82 119 94 248 257 221 211 c 0 0 0 0 0 233 132 13 0 0 555 592 591 0 0 3 140 206 238 176 94 95 136 132 g 0 0 0 0 0 74 146 47 2 34 0 0 0 0 0 135 24 38 69 89 90 91 53 76 t 0 0 0 0 0 104 153 122 28 0 0 0 0 592 0 0 212 266 166 233 160 149 182 173

TBP3_MA1355.1_JASPAR_shift1 (TBP3:MA1355.1:JASPAR) 0.720 0.532 7.826 0.925 0.903 6 3 2 4 6 4.200 5
; oligos_5-8nt_m2 versus TBP3_MA1355.1_JASPAR (TBP3:MA1355.1:JASPAR); m=5/6; ncol2=19; w=17; offset=-2; strand=D; shift=1; score= 4.2; -awwwhtwwrCCCTAAwtwy---- ; cor=0.720; Ncor=0.532; logoDP=7.826; NsEucl=0.925; NSW=0.903; rcor=6; rNcor=3; rlogoDP=2; rNsEucl=4; rNSW=6; rank_mean=4.200; match_rank=5 a 0 266 277 262 237 171 119 302 378 335 42 0 0 0 572 483 191 95 144 140 0 0 0 0 c 0 105 76 91 114 148 80 9 3 0 530 572 572 0 0 0 87 117 137 148 0 0 0 0 g 0 68 68 58 47 43 76 86 1 237 0 0 0 0 0 87 12 25 59 88 0 0 0 0 t 0 133 151 161 174 210 297 175 190 0 0 0 0 572 0 2 282 335 232 196 0 0 0 0

TBP3.ampDAP_M0621_AthalianaCistrome_rc_shift0 (TBP3.ampDAP:M0621:AthalianaCistrome_rc) 0.770 0.514 0.664 0.928 0.917 5 4 5 3 5 4.400 6
; oligos_5-8nt_m2 versus TBP3.ampDAP_M0621_AthalianaCistrome_rc (TBP3.ampDAP:M0621:AthalianaCistrome_rc); m=6/6; ncol2=19; w=16; offset=-3; strand=R; shift=0; score= 4.4; maamhhtaARCCCTAAwyy----- ; cor=0.770; Ncor=0.514; logoDP=0.664; NsEucl=0.928; NSW=0.917; rcor=5; rNcor=4; rlogoDP=5; rNsEucl=3; rNSW=5; rank_mean=4.400; match_rank=6 a 126 140 138 102 76 73 50 167 197 186 11 5 0 0 251 231 93 23 51 0 0 0 0 0 c 64 39 30 66 96 83 37 4 2 3 239 237 239 18 3 1 57 71 95 0 0 0 0 0 g 21 48 33 26 19 23 38 35 2 66 1 3 13 5 1 21 9 7 24 0 0 0 0 0 t 44 28 54 61 64 76 130 49 54 0 4 10 3 232 0 2 96 154 85 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m2_shift3 (oligos_5-8nt_m2)													; oligos_5-8nt_m2; m=0 (reference); ncol1=21; shift=3; ncol=24; ---bbcAAAACCCTAdtkmhcvwy ; Alignment reference a 0 0 0 1 1 2 14 16 15 16 0 0 0 1 12 4 3 3 4 4 1 4 7 3 c 0 0 0 4 6 9 0 0 0 0 14 16 16 1 2 2 3 3 10 4 9 4 3 5 g 0 0 0 5 4 2 2 0 1 0 1 0 0 0 1 6 1 6 1 2 3 5 1 3 t 0 0 0 6 5 3 0 0 0 0 1 0 0 14 1 4 9 4 1 6 3 3 5 5
AT1G72740_MA1353.1_JASPAR_shift4 (AT1G72740:MA1353.1:JASPAR)	0.849	0.607	10.200	0.935	0.936	3	2	1	2	3	2.200	1	; oligos_5-8nt_m2 versus AT1G72740_MA1353.1_JASPAR (AT1G72740:MA1353.1:JASPAR); m=1/6; ncol2=15; w=15; offset=1; strand=D; shift=4; score= 2.2; ----cctAAACCCTAAwyc----- ; cor=0.849; Ncor=0.607; logoDP=10.200; NsEucl=0.935; NSW=0.936; rcor=3; rNcor=2; rlogoDP=1; rNsEucl=2; rNSW=3; rank_mean=2.200; match_rank=1 a 0 0 0 0 62 69 59 214 282 282 10 0 0 0 289 242 138 9 37 0 0 0 0 0 c 0 0 0 0 154 159 46 3 3 0 281 291 291 0 0 0 41 129 157 0 0 0 0 0 g 0 0 0 0 23 34 51 22 2 9 0 0 0 0 1 49 2 16 27 0 0 0 0 0 t 0 0 0 0 52 29 135 52 4 0 0 0 0 291 1 0 110 137 70 0 0 0 0 0
AT1G72740.ampDAP_M0588_AthalianaCistrome_rc_shift5 (AT1G72740.ampDAP:M0588:AthalianaCistrome_rc)	0.841	0.695	0.622	0.948	0.948	4	1	6	1	1	2.600	2	; oligos_5-8nt_m2 versus AT1G72740.ampDAP_M0588_AthalianaCistrome_rc (AT1G72740.ampDAP:M0588:AthalianaCistrome_rc); m=2/6; ncol2=21; w=19; offset=2; strand=R; shift=5; score= 2.6; -----mwAAACCCTAAwyyywwww ; cor=0.841; Ncor=0.695; logoDP=0.622; NsEucl=0.948; NSW=0.948; rcor=4; rNcor=1; rlogoDP=6; rNsEucl=1; rNSW=1; rank_mean=2.600; match_rank=2 a 0 0 0 0 0 181 161 410 562 558 37 0 1 0 592 454 216 82 119 94 248 257 221 211 c 0 0 0 0 0 233 132 13 0 0 555 592 591 0 0 3 140 206 238 176 94 95 136 132 g 0 0 0 0 0 74 146 47 2 34 0 0 0 0 0 135 24 38 69 89 90 91 53 76 t 0 0 0 0 0 104 153 122 28 0 0 0 0 592 0 0 212 266 166 233 160 149 182 173
TBP3_MA1355.1_JASPAR_shift1 (TBP3:MA1355.1:JASPAR)	0.720	0.532	7.826	0.925	0.903	6	3	2	4	6	4.200	5	; oligos_5-8nt_m2 versus TBP3_MA1355.1_JASPAR (TBP3:MA1355.1:JASPAR); m=5/6; ncol2=19; w=17; offset=-2; strand=D; shift=1; score= 4.2; -awwwhtwwrCCCTAAwtwy---- ; cor=0.720; Ncor=0.532; logoDP=7.826; NsEucl=0.925; NSW=0.903; rcor=6; rNcor=3; rlogoDP=2; rNsEucl=4; rNSW=6; rank_mean=4.200; match_rank=5 a 0 266 277 262 237 171 119 302 378 335 42 0 0 0 572 483 191 95 144 140 0 0 0 0 c 0 105 76 91 114 148 80 9 3 0 530 572 572 0 0 0 87 117 137 148 0 0 0 0 g 0 68 68 58 47 43 76 86 1 237 0 0 0 0 0 87 12 25 59 88 0 0 0 0 t 0 133 151 161 174 210 297 175 190 0 0 0 0 572 0 2 282 335 232 196 0 0 0 0
TBP3.ampDAP_M0621_AthalianaCistrome_rc_shift0 (TBP3.ampDAP:M0621:AthalianaCistrome_rc)	0.770	0.514	0.664	0.928	0.917	5	4	5	3	5	4.400	6	; oligos_5-8nt_m2 versus TBP3.ampDAP_M0621_AthalianaCistrome_rc (TBP3.ampDAP:M0621:AthalianaCistrome_rc); m=6/6; ncol2=19; w=16; offset=-3; strand=R; shift=0; score= 4.4; maamhhtaARCCCTAAwyy----- ; cor=0.770; Ncor=0.514; logoDP=0.664; NsEucl=0.928; NSW=0.917; rcor=5; rNcor=4; rlogoDP=5; rNsEucl=3; rNSW=5; rank_mean=4.400; match_rank=6 a 126 140 138 102 76 73 50 167 197 186 11 5 0 0 251 231 93 23 51 0 0 0 0 0 c 64 39 30 66 96 83 37 4 2 3 239 237 239 18 3 1 57 71 95 0 0 0 0 0 g 21 48 33 26 19 23 38 35 2 66 1 3 13 5 1 21 9 7 24 0 0 0 0 0 t 44 28 54 61 64 76 130 49 54 0 4 10 3 232 0 2 96 154 85 0 0 0 0 0