One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/02/compare-matrices_2019-07-02.133508_l0C4xe/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_2019-07-02.133508_l0C4xe/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift10 ; 14 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_shift10 (oligos_5-8nt_m1)
; oligos_5-8nt_m1; m=0 (reference); ncol1=19; shift=10; ncol=30; ----------maacCCcAAAACCCtaawh- ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 81 71 106 45 17 13 24 144 181 184 178 11 5 8 40 110 73 75 52 0 c 0 0 0 0 0 0 0 0 0 0 67 48 37 96 142 156 130 26 4 2 10 170 177 174 20 38 33 45 57 0 g 0 0 0 0 0 0 0 0 0 0 16 27 17 12 6 12 10 10 2 2 2 7 5 5 11 17 45 22 30 0 t 0 0 0 0 0 0 0 0 0 0 30 48 34 41 29 13 30 14 7 6 4 6 7 7 123 29 43 52 55 0

AT1G72740_MA1353.1_JASPAR_shift15 (AT1G72740:MA1353.1:JASPAR) 0.867 0.607 6.880 0.936 0.943 2 4 6 2 2 3.200 1
; oligos_5-8nt_m1 versus AT1G72740_MA1353.1_JASPAR (AT1G72740:MA1353.1:JASPAR); m=1/13; ncol2=15; w=14; offset=5; strand=D; shift=15; score= 3.2; ---------------cctAAACCCTAAwyc ; cor=0.867; Ncor=0.607; logoDP=6.880; NsEucl=0.936; NSW=0.943; rcor=2; rNcor=4; rlogoDP=6; rNsEucl=2; rNSW=2; rank_mean=3.200; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 69 59 214 282 282 10 0 0 0 289 242 138 9 37 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 154 159 46 3 3 0 281 291 291 0 0 0 41 129 157 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 34 51 22 2 9 0 0 0 0 1 49 2 16 27 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52 29 135 52 4 0 0 0 0 291 1 0 110 137 70

TRP2.ampDAP_M0612_AthalianaCistrome_shift11 (TRP2.ampDAP:M0612:AthalianaCistrome) 0.810 0.663 8.681 0.925 0.899 5 3 1 4 8 4.200 2
; oligos_5-8nt_m1 versus TRP2.ampDAP_M0612_AthalianaCistrome (TRP2.ampDAP:M0612:AthalianaCistrome); m=2/13; ncol2=21; w=18; offset=1; strand=D; shift=11; score= 4.2; -----------AAACCCTAAACCCTAAACC ; cor=0.810; Ncor=0.663; logoDP=8.681; NsEucl=0.925; NSW=0.899; rcor=5; rNcor=3; rlogoDP=1; rNsEucl=4; rNSW=8; rank_mean=4.200; match_rank=2 a 0 0 0 0 0 0 0 0 0 0 0 90 85 87 0 9 7 12 103 104 101 2 1 0 5 99 99 97 7 14 c 0 0 0 0 0 0 0 0 0 0 0 3 2 1 85 88 75 2 0 0 3 102 103 102 0 0 0 0 80 75 g 0 0 0 0 0 0 0 0 0 0 0 2 4 1 5 5 5 1 1 0 0 0 0 0 0 4 3 2 1 1 t 0 0 0 0 0 0 0 0 0 0 0 9 13 15 14 2 17 89 0 0 0 0 0 2 99 1 2 5 16 14

TRP2_MA1356.1_JASPAR_shift11 (TRP2:MA1356.1:JASPAR) 0.779 0.668 8.482 0.916 0.874 8 2 2 11 10 6.600 6
; oligos_5-8nt_m1 versus TRP2_MA1356.1_JASPAR (TRP2:MA1356.1:JASPAR); m=6/13; ncol2=20; w=18; offset=1; strand=D; shift=11; score= 6.6; -----------AAACCCTAAACCCTAAACC ; cor=0.779; Ncor=0.668; logoDP=8.482; NsEucl=0.916; NSW=0.874; rcor=8; rNcor=2; rlogoDP=2; rNsEucl=11; rNSW=10; rank_mean=6.600; match_rank=6 a 0 0 0 0 0 0 0 0 0 0 0 72 72 72 0 6 0 3 72 76 75 0 2 2 2 73 68 73 1 7 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 66 63 65 1 0 0 0 75 74 71 0 0 6 0 69 62 g 0 0 0 0 0 0 0 0 0 0 0 1 2 0 2 2 1 1 0 0 0 1 0 3 3 1 0 2 0 2 t 0 0 0 0 0 0 0 0 0 0 0 3 2 4 8 5 10 71 4 0 1 0 0 0 71 2 2 1 6 5

TBP3.ampDAP_M0621_AthalianaCistrome_rc_shift11 (TBP3.ampDAP:M0621:AthalianaCistrome_rc) 0.751 0.676 0.567 0.935 0.924 11 1 12 3 7 6.800 7
; oligos_5-8nt_m1 versus TBP3.ampDAP_M0621_AthalianaCistrome_rc (TBP3.ampDAP:M0621:AthalianaCistrome_rc); m=7/13; ncol2=19; w=18; offset=1; strand=R; shift=11; score= 6.8; -----------maamhhtaARCCCTAAwyy ; cor=0.751; Ncor=0.676; logoDP=0.567; NsEucl=0.935; NSW=0.924; rcor=11; rNcor=1; rlogoDP=12; rNsEucl=3; rNSW=7; rank_mean=6.800; match_rank=7 a 0 0 0 0 0 0 0 0 0 0 0 126 140 138 102 76 73 50 167 197 186 11 5 0 0 251 231 93 23 51 c 0 0 0 0 0 0 0 0 0 0 0 64 39 30 66 96 83 37 4 2 3 239 237 239 18 3 1 57 71 95 g 0 0 0 0 0 0 0 0 0 0 0 21 48 33 26 19 23 38 35 2 66 1 3 13 5 1 21 9 7 24 t 0 0 0 0 0 0 0 0 0 0 0 44 28 54 61 64 76 130 49 54 0 4 10 3 232 0 2 96 154 85

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_5-8nt_m1_shift10 (oligos_5-8nt_m1)													; oligos_5-8nt_m1; m=0 (reference); ncol1=19; shift=10; ncol=30; ----------maacCCcAAAACCCtaawh- ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 81 71 106 45 17 13 24 144 181 184 178 11 5 8 40 110 73 75 52 0 c 0 0 0 0 0 0 0 0 0 0 67 48 37 96 142 156 130 26 4 2 10 170 177 174 20 38 33 45 57 0 g 0 0 0 0 0 0 0 0 0 0 16 27 17 12 6 12 10 10 2 2 2 7 5 5 11 17 45 22 30 0 t 0 0 0 0 0 0 0 0 0 0 30 48 34 41 29 13 30 14 7 6 4 6 7 7 123 29 43 52 55 0
AT1G72740_MA1353.1_JASPAR_shift15 (AT1G72740:MA1353.1:JASPAR)	0.867	0.607	6.880	0.936	0.943	2	4	6	2	2	3.200	1	; oligos_5-8nt_m1 versus AT1G72740_MA1353.1_JASPAR (AT1G72740:MA1353.1:JASPAR); m=1/13; ncol2=15; w=14; offset=5; strand=D; shift=15; score= 3.2; ---------------cctAAACCCTAAwyc ; cor=0.867; Ncor=0.607; logoDP=6.880; NsEucl=0.936; NSW=0.943; rcor=2; rNcor=4; rlogoDP=6; rNsEucl=2; rNSW=2; rank_mean=3.200; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 69 59 214 282 282 10 0 0 0 289 242 138 9 37 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 154 159 46 3 3 0 281 291 291 0 0 0 41 129 157 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 34 51 22 2 9 0 0 0 0 1 49 2 16 27 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52 29 135 52 4 0 0 0 0 291 1 0 110 137 70
TRP2.ampDAP_M0612_AthalianaCistrome_shift11 (TRP2.ampDAP:M0612:AthalianaCistrome)	0.810	0.663	8.681	0.925	0.899	5	3	1	4	8	4.200	2	; oligos_5-8nt_m1 versus TRP2.ampDAP_M0612_AthalianaCistrome (TRP2.ampDAP:M0612:AthalianaCistrome); m=2/13; ncol2=21; w=18; offset=1; strand=D; shift=11; score= 4.2; -----------AAACCCTAAACCCTAAACC ; cor=0.810; Ncor=0.663; logoDP=8.681; NsEucl=0.925; NSW=0.899; rcor=5; rNcor=3; rlogoDP=1; rNsEucl=4; rNSW=8; rank_mean=4.200; match_rank=2 a 0 0 0 0 0 0 0 0 0 0 0 90 85 87 0 9 7 12 103 104 101 2 1 0 5 99 99 97 7 14 c 0 0 0 0 0 0 0 0 0 0 0 3 2 1 85 88 75 2 0 0 3 102 103 102 0 0 0 0 80 75 g 0 0 0 0 0 0 0 0 0 0 0 2 4 1 5 5 5 1 1 0 0 0 0 0 0 4 3 2 1 1 t 0 0 0 0 0 0 0 0 0 0 0 9 13 15 14 2 17 89 0 0 0 0 0 2 99 1 2 5 16 14
TRP2_MA1356.1_JASPAR_shift11 (TRP2:MA1356.1:JASPAR)	0.779	0.668	8.482	0.916	0.874	8	2	2	11	10	6.600	6	; oligos_5-8nt_m1 versus TRP2_MA1356.1_JASPAR (TRP2:MA1356.1:JASPAR); m=6/13; ncol2=20; w=18; offset=1; strand=D; shift=11; score= 6.6; -----------AAACCCTAAACCCTAAACC ; cor=0.779; Ncor=0.668; logoDP=8.482; NsEucl=0.916; NSW=0.874; rcor=8; rNcor=2; rlogoDP=2; rNsEucl=11; rNSW=10; rank_mean=6.600; match_rank=6 a 0 0 0 0 0 0 0 0 0 0 0 72 72 72 0 6 0 3 72 76 75 0 2 2 2 73 68 73 1 7 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 66 63 65 1 0 0 0 75 74 71 0 0 6 0 69 62 g 0 0 0 0 0 0 0 0 0 0 0 1 2 0 2 2 1 1 0 0 0 1 0 3 3 1 0 2 0 2 t 0 0 0 0 0 0 0 0 0 0 0 3 2 4 8 5 10 71 4 0 1 0 0 0 71 2 2 1 6 5
TBP3.ampDAP_M0621_AthalianaCistrome_rc_shift11 (TBP3.ampDAP:M0621:AthalianaCistrome_rc)	0.751	0.676	0.567	0.935	0.924	11	1	12	3	7	6.800	7	; oligos_5-8nt_m1 versus TBP3.ampDAP_M0621_AthalianaCistrome_rc (TBP3.ampDAP:M0621:AthalianaCistrome_rc); m=7/13; ncol2=19; w=18; offset=1; strand=R; shift=11; score= 6.8; -----------maamhhtaARCCCTAAwyy ; cor=0.751; Ncor=0.676; logoDP=0.567; NsEucl=0.935; NSW=0.924; rcor=11; rNcor=1; rlogoDP=12; rNsEucl=3; rNSW=7; rank_mean=6.800; match_rank=7 a 0 0 0 0 0 0 0 0 0 0 0 126 140 138 102 76 73 50 167 197 186 11 5 0 0 251 231 93 23 51 c 0 0 0 0 0 0 0 0 0 0 0 64 39 30 66 96 83 37 4 2 3 239 237 239 18 3 1 57 71 95 g 0 0 0 0 0 0 0 0 0 0 0 21 48 33 26 19 23 38 35 2 66 1 3 13 5 1 21 9 7 24 t 0 0 0 0 0 0 0 0 0 0 0 44 28 54 61 64 76 130 49 54 0 4 10 3 232 0 2 96 154 85