One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/07/compare-matrices_2019-07-07.130048_b9Qm0C/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_2019-07-07.130048_b9Qm0C/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m2_shift0 ; 45 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_shift0 (oligos_5-8nt_m2)
; oligos_5-8nt_m2; m=0 (reference); ncol1=24; shift=0; ncol=27; gwkkygGACACGTGgCgrmmkrkk--- ; Alignment reference a 15 26 20 16 18 11 9 62 1 84 1 6 0 0 3 8 20 23 25 30 20 24 17 18 0 0 0 c 18 14 15 13 24 17 6 18 76 0 83 2 1 0 5 66 9 19 27 26 16 21 19 19 0 0 0 g 33 21 24 33 21 39 68 2 5 3 1 79 1 87 58 5 45 25 20 12 26 28 24 27 0 0 0 t 21 26 28 25 24 20 4 5 5 0 2 0 85 0 21 8 13 20 15 19 25 14 27 23 0 0 0

ABF1_MA0570.1_JASPAR_shift5 (ABF1:MA0570.1:JASPAR) 0.901 0.714 9.585 0.958 0.967 7 3 2 4 6 4.400 1
; oligos_5-8nt_m2 versus ABF1_MA0570.1_JASPAR (ABF1:MA0570.1:JASPAR); m=1/44; ncol2=19; w=19; offset=5; strand=D; shift=5; score= 4.4; -----GgmCACGTGGCmcrvvvgr--- ; cor=0.901; Ncor=0.714; logoDP=9.585; NsEucl=0.958; NSW=0.967; rcor=7; rNcor=3; rlogoDP=2; rNsEucl=4; rNSW=6; rank_mean=4.400; match_rank=1 a 0 0 0 0 0 0 8 19 0 43 0 0 0 0 0 0 17 6 13 20 12 13 10 13 0 0 0 c 0 0 0 0 0 4 2 16 35 0 44 0 0 0 0 44 14 24 6 11 19 12 6 9 0 0 0 g 0 0 0 0 0 32 28 0 8 1 0 44 0 44 38 0 9 9 21 11 13 17 23 20 0 0 0 t 0 0 0 0 0 8 6 9 1 0 0 0 44 0 6 0 4 5 4 2 0 2 5 2 0 0 0

bHLH34.DAP_M0166_AthalianaCistrome_shift0 (bHLH34.DAP:M0166:AthalianaCistrome) 0.857 0.822 7.735 0.962 0.967 22 1 24 2 5 10.800 5
; oligos_5-8nt_m2 versus bHLH34.DAP_M0166_AthalianaCistrome (bHLH34.DAP:M0166:AthalianaCistrome); m=5/44; ncol2=23; w=23; offset=0; strand=D; shift=0; score= 10.8; gtgrwwgrCACGTGycarcwygw---- ; cor=0.857; Ncor=0.822; logoDP=7.735; NsEucl=0.962; NSW=0.967; rcor=22; rNcor=1; rlogoDP=24; rNsEucl=2; rNSW=5; rank_mean=10.800; match_rank=5 a 118 123 108 154 180 152 140 205 7 549 0 45 13 0 65 89 224 182 139 203 86 136 162 0 0 0 0 c 68 69 37 124 119 124 72 135 560 6 567 0 68 0 188 308 87 99 213 101 202 105 104 0 0 0 0 g 329 62 365 162 101 122 242 153 0 9 0 522 2 559 117 85 132 152 105 106 106 211 97 0 0 0 0 t 52 313 57 127 167 169 113 74 0 3 0 0 484 8 197 85 124 134 110 157 173 115 204 0 0 0 0

bHLH31_MA1359.1_JASPAR_rc_shift0 (bHLH31:MA1359.1:JASPAR_rc) 0.834 0.730 0.248 0.956 0.959 24 2 43 6 12 17.400 14
; oligos_5-8nt_m2 versus bHLH31_MA1359.1_JASPAR_rc (bHLH31:MA1359.1:JASPAR_rc); m=14/44; ncol2=21; w=21; offset=0; strand=R; shift=0; score= 17.4; gwgwwwsvCACGTGycwcmws------ ; cor=0.834; Ncor=0.730; logoDP=0.248; NsEucl=0.956; NSW=0.959; rcor=24; rNcor=2; rlogoDP=43; rNsEucl=6; rNSW=12; rank_mean=17.400; match_rank=14 a 123 160 91 258 190 170 137 165 0 595 0 14 0 0 106 107 232 129 172 234 63 0 0 0 0 0 0 c 115 83 146 87 97 94 163 180 595 0 547 0 0 0 194 231 83 230 204 54 215 0 0 0 0 0 0 g 259 101 257 95 121 141 182 167 0 0 0 581 0 595 142 131 116 100 122 44 179 0 0 0 0 0 0 t 98 251 101 155 187 190 113 83 0 0 48 0 595 0 153 126 164 136 97 263 138 0 0 0 0 0 0

bHLH74_MA1360.1_JASPAR_rc_shift2 (bHLH74:MA1360.1:JASPAR_rc) 0.752 0.658 0.763 0.945 0.936 37 4 35 18 28 24.400 26
; oligos_5-8nt_m2 versus bHLH74_MA1360.1_JASPAR_rc (bHLH74:MA1360.1:JASPAR_rc); m=26/44; ncol2=21; w=21; offset=2; strand=R; shift=2; score= 24.4; --wgrtskCACGTGmywytcacg---- ; cor=0.752; Ncor=0.658; logoDP=0.763; NsEucl=0.945; NSW=0.936; rcor=37; rNcor=4; rlogoDP=35; rNsEucl=18; rNSW=28; rank_mean=24.400; match_rank=26 a 0 0 86 36 58 48 49 24 0 198 6 0 0 0 51 25 63 48 45 12 106 38 23 0 0 0 0 c 0 0 18 36 42 48 52 32 198 0 191 0 0 5 72 63 48 58 30 124 24 100 47 0 0 0 0 g 0 0 11 87 60 38 66 68 0 0 0 198 0 193 49 37 23 32 23 40 30 18 103 0 0 0 0 t 0 0 83 39 38 64 31 74 0 0 1 0 198 0 26 73 64 60 100 22 38 42 25 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_shift0 (oligos_5-8nt_m2)													; oligos_5-8nt_m2; m=0 (reference); ncol1=24; shift=0; ncol=27; gwkkygGACACGTGgCgrmmkrkk--- ; Alignment reference a 15 26 20 16 18 11 9 62 1 84 1 6 0 0 3 8 20 23 25 30 20 24 17 18 0 0 0 c 18 14 15 13 24 17 6 18 76 0 83 2 1 0 5 66 9 19 27 26 16 21 19 19 0 0 0 g 33 21 24 33 21 39 68 2 5 3 1 79 1 87 58 5 45 25 20 12 26 28 24 27 0 0 0 t 21 26 28 25 24 20 4 5 5 0 2 0 85 0 21 8 13 20 15 19 25 14 27 23 0 0 0
ABF1_MA0570.1_JASPAR_shift5 (ABF1:MA0570.1:JASPAR)	0.901	0.714	9.585	0.958	0.967	7	3	2	4	6	4.400	1	; oligos_5-8nt_m2 versus ABF1_MA0570.1_JASPAR (ABF1:MA0570.1:JASPAR); m=1/44; ncol2=19; w=19; offset=5; strand=D; shift=5; score= 4.4; -----GgmCACGTGGCmcrvvvgr--- ; cor=0.901; Ncor=0.714; logoDP=9.585; NsEucl=0.958; NSW=0.967; rcor=7; rNcor=3; rlogoDP=2; rNsEucl=4; rNSW=6; rank_mean=4.400; match_rank=1 a 0 0 0 0 0 0 8 19 0 43 0 0 0 0 0 0 17 6 13 20 12 13 10 13 0 0 0 c 0 0 0 0 0 4 2 16 35 0 44 0 0 0 0 44 14 24 6 11 19 12 6 9 0 0 0 g 0 0 0 0 0 32 28 0 8 1 0 44 0 44 38 0 9 9 21 11 13 17 23 20 0 0 0 t 0 0 0 0 0 8 6 9 1 0 0 0 44 0 6 0 4 5 4 2 0 2 5 2 0 0 0
bHLH34.DAP_M0166_AthalianaCistrome_shift0 (bHLH34.DAP:M0166:AthalianaCistrome)	0.857	0.822	7.735	0.962	0.967	22	1	24	2	5	10.800	5	; oligos_5-8nt_m2 versus bHLH34.DAP_M0166_AthalianaCistrome (bHLH34.DAP:M0166:AthalianaCistrome); m=5/44; ncol2=23; w=23; offset=0; strand=D; shift=0; score= 10.8; gtgrwwgrCACGTGycarcwygw---- ; cor=0.857; Ncor=0.822; logoDP=7.735; NsEucl=0.962; NSW=0.967; rcor=22; rNcor=1; rlogoDP=24; rNsEucl=2; rNSW=5; rank_mean=10.800; match_rank=5 a 118 123 108 154 180 152 140 205 7 549 0 45 13 0 65 89 224 182 139 203 86 136 162 0 0 0 0 c 68 69 37 124 119 124 72 135 560 6 567 0 68 0 188 308 87 99 213 101 202 105 104 0 0 0 0 g 329 62 365 162 101 122 242 153 0 9 0 522 2 559 117 85 132 152 105 106 106 211 97 0 0 0 0 t 52 313 57 127 167 169 113 74 0 3 0 0 484 8 197 85 124 134 110 157 173 115 204 0 0 0 0
bHLH31_MA1359.1_JASPAR_rc_shift0 (bHLH31:MA1359.1:JASPAR_rc)	0.834	0.730	0.248	0.956	0.959	24	2	43	6	12	17.400	14	; oligos_5-8nt_m2 versus bHLH31_MA1359.1_JASPAR_rc (bHLH31:MA1359.1:JASPAR_rc); m=14/44; ncol2=21; w=21; offset=0; strand=R; shift=0; score= 17.4; gwgwwwsvCACGTGycwcmws------ ; cor=0.834; Ncor=0.730; logoDP=0.248; NsEucl=0.956; NSW=0.959; rcor=24; rNcor=2; rlogoDP=43; rNsEucl=6; rNSW=12; rank_mean=17.400; match_rank=14 a 123 160 91 258 190 170 137 165 0 595 0 14 0 0 106 107 232 129 172 234 63 0 0 0 0 0 0 c 115 83 146 87 97 94 163 180 595 0 547 0 0 0 194 231 83 230 204 54 215 0 0 0 0 0 0 g 259 101 257 95 121 141 182 167 0 0 0 581 0 595 142 131 116 100 122 44 179 0 0 0 0 0 0 t 98 251 101 155 187 190 113 83 0 0 48 0 595 0 153 126 164 136 97 263 138 0 0 0 0 0 0
bHLH74_MA1360.1_JASPAR_rc_shift2 (bHLH74:MA1360.1:JASPAR_rc)	0.752	0.658	0.763	0.945	0.936	37	4	35	18	28	24.400	26	; oligos_5-8nt_m2 versus bHLH74_MA1360.1_JASPAR_rc (bHLH74:MA1360.1:JASPAR_rc); m=26/44; ncol2=21; w=21; offset=2; strand=R; shift=2; score= 24.4; --wgrtskCACGTGmywytcacg---- ; cor=0.752; Ncor=0.658; logoDP=0.763; NsEucl=0.945; NSW=0.936; rcor=37; rNcor=4; rlogoDP=35; rNsEucl=18; rNSW=28; rank_mean=24.400; match_rank=26 a 0 0 86 36 58 48 49 24 0 198 6 0 0 0 51 25 63 48 45 12 106 38 23 0 0 0 0 c 0 0 18 36 42 48 52 32 198 0 191 0 0 5 72 63 48 58 30 124 24 100 47 0 0 0 0 g 0 0 11 87 60 38 66 68 0 0 0 198 0 193 49 37 23 32 23 40 30 18 103 0 0 0 0 t 0 0 83 39 38 64 31 74 0 0 1 0 198 0 26 73 64 60 100 22 38 42 25 0 0 0 0