One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/08/compare-matrices_2019-07-08.175359_zWE5jw/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/2019/07/08/compare-matrices_2019-07-08.175359_zWE5jw/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift5 ; 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_shift5 (oligos_5-8nt_m1)
; oligos_5-8nt_m1; m=0 (reference); ncol1=22; shift=5; ncol=30; -----whcCtAAAACCCTAAamcCcmh--- ; Alignment reference a 0 0 0 0 0 76 60 52 24 39 161 206 208 199 4 5 9 36 175 163 138 58 39 28 42 86 75 0 0 0 c 0 0 0 0 0 54 68 94 162 50 13 8 6 14 208 204 203 17 16 24 47 121 136 153 106 57 57 0 0 0 g 0 0 0 0 0 29 24 35 19 14 6 6 3 3 7 5 4 5 13 25 11 12 11 15 22 27 35 0 0 0 t 0 0 0 0 0 65 72 43 19 121 44 4 7 8 5 10 8 166 20 12 28 33 38 28 54 54 57 0 0 0

TRP2.ampDAP_M0612_AthalianaCistrome_shift4 (TRP2.ampDAP:M0612:AthalianaCistrome) 0.850 0.739 9.653 0.938 0.922 3 2 1 4 5 3.000 1
; oligos_5-8nt_m1 versus TRP2.ampDAP_M0612_AthalianaCistrome (TRP2.ampDAP:M0612:AthalianaCistrome); m=1/13; ncol2=21; w=20; offset=-1; strand=D; shift=4; score= 3; ----AAACCCTAAACCCTAAACCCT----- ; cor=0.850; Ncor=0.739; logoDP=9.653; NsEucl=0.938; NSW=0.922; rcor=3; rNcor=2; rlogoDP=1; rNsEucl=4; rNSW=5; rank_mean=3.000; match_rank=1 a 0 0 0 0 90 85 87 0 9 7 12 103 104 101 2 1 0 5 99 99 97 7 14 4 11 0 0 0 0 0 c 0 0 0 0 3 2 1 85 88 75 2 0 0 3 102 103 102 0 0 0 0 80 75 76 10 0 0 0 0 0 g 0 0 0 0 2 4 1 5 5 5 1 1 0 0 0 0 0 0 4 3 2 1 1 1 5 0 0 0 0 0 t 0 0 0 0 9 13 15 14 2 17 89 0 0 0 0 0 2 99 1 2 5 16 14 23 78 0 0 0 0 0

TRP2_MA1356.1_JASPAR_shift4 (TRP2:MA1356.1:JASPAR) 0.830 0.686 9.302 0.928 0.903 5 4 3 6 7 5.000 4
; oligos_5-8nt_m1 versus TRP2_MA1356.1_JASPAR (TRP2:MA1356.1:JASPAR); m=4/13; ncol2=20; w=19; offset=-1; strand=D; shift=4; score= 5; ----AAACCCTAAACCCTAAACCC------ ; cor=0.830; Ncor=0.686; logoDP=9.302; NsEucl=0.928; NSW=0.903; rcor=5; rNcor=4; rlogoDP=3; rNsEucl=6; rNSW=7; rank_mean=5.000; match_rank=4 a 0 0 0 0 72 72 72 0 6 0 3 72 76 75 0 2 2 2 73 68 73 1 7 7 0 0 0 0 0 0 c 0 0 0 0 0 0 0 66 63 65 1 0 0 0 75 74 71 0 0 6 0 69 62 61 0 0 0 0 0 0 g 0 0 0 0 1 2 0 2 2 1 1 0 0 0 1 0 3 3 1 0 2 0 2 2 0 0 0 0 0 0 t 0 0 0 0 3 2 4 8 5 10 71 4 0 1 0 0 0 71 2 2 1 6 5 6 0 0 0 0 0 0

TRP1_MA1352.1_JASPAR_shift4 (TRP1:MA1352.1:JASPAR) 0.775 0.741 9.325 0.924 0.873 6 1 2 9 11 5.800 6
; oligos_5-8nt_m1 versus TRP1_MA1352.1_JASPAR (TRP1:MA1352.1:JASPAR); m=6/13; ncol2=23; w=22; offset=-1; strand=D; shift=4; score= 5.8; ----AAACCCTAAACCCTAAACCCTAA--- ; cor=0.775; Ncor=0.741; logoDP=9.325; NsEucl=0.924; NSW=0.873; rcor=6; rNcor=1; rlogoDP=2; rNsEucl=9; rNSW=11; rank_mean=5.800; match_rank=6 a 0 0 0 0 45 44 47 0 5 2 0 47 47 48 0 4 0 1 47 43 46 0 8 3 2 47 44 0 0 0 c 0 0 0 0 0 0 0 44 39 36 0 0 0 0 43 43 47 0 0 2 0 43 39 45 1 0 0 0 0 0 g 0 0 0 0 0 0 0 1 2 5 0 0 1 0 0 0 1 0 0 0 2 1 0 0 0 0 0 0 0 0 t 0 0 0 0 3 4 1 3 2 5 48 1 0 0 5 1 0 47 1 3 0 4 1 0 45 1 4 0 0 0

SRS7.DAP_M0745_AthalianaCistrome_shift4 (SRS7.DAP:M0745:AthalianaCistrome) 0.739 0.707 7.325 0.923 0.869 10 3 6 10 12 8.200 8
; oligos_5-8nt_m1 versus SRS7.DAP_M0745_AthalianaCistrome (SRS7.DAP:M0745:AthalianaCistrome); m=8/13; ncol2=23; w=22; offset=-1; strand=D; shift=4; score= 8.2; ----AAACCCTAAACCCTAAACCCTAA--- ; cor=0.739; Ncor=0.707; logoDP=7.325; NsEucl=0.923; NSW=0.869; rcor=10; rNcor=3; rlogoDP=6; rNsEucl=10; rNSW=12; rank_mean=8.200; match_rank=8 a 0 0 0 0 24 22 25 0 0 2 0 23 21 22 1 2 0 0 24 17 23 2 0 0 2 25 22 0 0 0 c 0 0 0 0 0 0 0 22 24 23 0 0 0 0 22 21 21 0 0 0 1 21 22 23 0 0 0 0 0 0 g 0 0 0 0 0 1 0 1 1 0 0 0 1 1 1 0 1 0 0 4 0 0 0 0 0 0 2 0 0 0 t 0 0 0 0 1 2 0 2 0 0 25 2 3 2 1 2 3 25 1 4 1 2 3 2 23 0 1 0 0 0

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=30; -----whcCtAAAACCCTAAamcCcmh--- ; Alignment reference a 0 0 0 0 0 76 60 52 24 39 161 206 208 199 4 5 9 36 175 163 138 58 39 28 42 86 75 0 0 0 c 0 0 0 0 0 54 68 94 162 50 13 8 6 14 208 204 203 17 16 24 47 121 136 153 106 57 57 0 0 0 g 0 0 0 0 0 29 24 35 19 14 6 6 3 3 7 5 4 5 13 25 11 12 11 15 22 27 35 0 0 0 t 0 0 0 0 0 65 72 43 19 121 44 4 7 8 5 10 8 166 20 12 28 33 38 28 54 54 57 0 0 0
TRP2.ampDAP_M0612_AthalianaCistrome_shift4 (TRP2.ampDAP:M0612:AthalianaCistrome)	0.850	0.739	9.653	0.938	0.922	3	2	1	4	5	3.000	1	; oligos_5-8nt_m1 versus TRP2.ampDAP_M0612_AthalianaCistrome (TRP2.ampDAP:M0612:AthalianaCistrome); m=1/13; ncol2=21; w=20; offset=-1; strand=D; shift=4; score= 3; ----AAACCCTAAACCCTAAACCCT----- ; cor=0.850; Ncor=0.739; logoDP=9.653; NsEucl=0.938; NSW=0.922; rcor=3; rNcor=2; rlogoDP=1; rNsEucl=4; rNSW=5; rank_mean=3.000; match_rank=1 a 0 0 0 0 90 85 87 0 9 7 12 103 104 101 2 1 0 5 99 99 97 7 14 4 11 0 0 0 0 0 c 0 0 0 0 3 2 1 85 88 75 2 0 0 3 102 103 102 0 0 0 0 80 75 76 10 0 0 0 0 0 g 0 0 0 0 2 4 1 5 5 5 1 1 0 0 0 0 0 0 4 3 2 1 1 1 5 0 0 0 0 0 t 0 0 0 0 9 13 15 14 2 17 89 0 0 0 0 0 2 99 1 2 5 16 14 23 78 0 0 0 0 0
TRP2_MA1356.1_JASPAR_shift4 (TRP2:MA1356.1:JASPAR)	0.830	0.686	9.302	0.928	0.903	5	4	3	6	7	5.000	4	; oligos_5-8nt_m1 versus TRP2_MA1356.1_JASPAR (TRP2:MA1356.1:JASPAR); m=4/13; ncol2=20; w=19; offset=-1; strand=D; shift=4; score= 5; ----AAACCCTAAACCCTAAACCC------ ; cor=0.830; Ncor=0.686; logoDP=9.302; NsEucl=0.928; NSW=0.903; rcor=5; rNcor=4; rlogoDP=3; rNsEucl=6; rNSW=7; rank_mean=5.000; match_rank=4 a 0 0 0 0 72 72 72 0 6 0 3 72 76 75 0 2 2 2 73 68 73 1 7 7 0 0 0 0 0 0 c 0 0 0 0 0 0 0 66 63 65 1 0 0 0 75 74 71 0 0 6 0 69 62 61 0 0 0 0 0 0 g 0 0 0 0 1 2 0 2 2 1 1 0 0 0 1 0 3 3 1 0 2 0 2 2 0 0 0 0 0 0 t 0 0 0 0 3 2 4 8 5 10 71 4 0 1 0 0 0 71 2 2 1 6 5 6 0 0 0 0 0 0
TRP1_MA1352.1_JASPAR_shift4 (TRP1:MA1352.1:JASPAR)	0.775	0.741	9.325	0.924	0.873	6	1	2	9	11	5.800	6	; oligos_5-8nt_m1 versus TRP1_MA1352.1_JASPAR (TRP1:MA1352.1:JASPAR); m=6/13; ncol2=23; w=22; offset=-1; strand=D; shift=4; score= 5.8; ----AAACCCTAAACCCTAAACCCTAA--- ; cor=0.775; Ncor=0.741; logoDP=9.325; NsEucl=0.924; NSW=0.873; rcor=6; rNcor=1; rlogoDP=2; rNsEucl=9; rNSW=11; rank_mean=5.800; match_rank=6 a 0 0 0 0 45 44 47 0 5 2 0 47 47 48 0 4 0 1 47 43 46 0 8 3 2 47 44 0 0 0 c 0 0 0 0 0 0 0 44 39 36 0 0 0 0 43 43 47 0 0 2 0 43 39 45 1 0 0 0 0 0 g 0 0 0 0 0 0 0 1 2 5 0 0 1 0 0 0 1 0 0 0 2 1 0 0 0 0 0 0 0 0 t 0 0 0 0 3 4 1 3 2 5 48 1 0 0 5 1 0 47 1 3 0 4 1 0 45 1 4 0 0 0
SRS7.DAP_M0745_AthalianaCistrome_shift4 (SRS7.DAP:M0745:AthalianaCistrome)	0.739	0.707	7.325	0.923	0.869	10	3	6	10	12	8.200	8	; oligos_5-8nt_m1 versus SRS7.DAP_M0745_AthalianaCistrome (SRS7.DAP:M0745:AthalianaCistrome); m=8/13; ncol2=23; w=22; offset=-1; strand=D; shift=4; score= 8.2; ----AAACCCTAAACCCTAAACCCTAA--- ; cor=0.739; Ncor=0.707; logoDP=7.325; NsEucl=0.923; NSW=0.869; rcor=10; rNcor=3; rlogoDP=6; rNsEucl=10; rNSW=12; rank_mean=8.200; match_rank=8 a 0 0 0 0 24 22 25 0 0 2 0 23 21 22 1 2 0 0 24 17 23 2 0 0 2 25 22 0 0 0 c 0 0 0 0 0 0 0 22 24 23 0 0 0 0 22 21 21 0 0 0 1 21 22 23 0 0 0 0 0 0 g 0 0 0 0 0 1 0 1 1 0 0 0 1 1 1 0 1 0 0 4 0 0 0 0 0 0 2 0 0 0 t 0 0 0 0 1 2 0 2 0 0 25 2 3 2 1 2 3 25 1 4 1 2 3 2 23 0 1 0 0 0