One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 7 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=15; shift=0; ncol=18; wrCAAATATTTACwt--- ; Alignment reference a 135 121 19 289 293 299 0 299 3 1 5 274 23 88 77 0 0 0 c 38 35 257 10 6 2 6 0 2 1 2 2 230 64 76 0 0 0 g 54 88 7 0 3 3 4 9 4 2 11 18 10 20 69 0 0 0 t 82 65 26 10 7 5 299 1 300 305 291 15 46 137 87 0 0 0

MA0047.2_shift6 (Foxa2) 0.860 0.430 6.826 0.417 0.913 1.223 0.932 1 2 1 2 1 1 1 1.286 1
; dyads_m2 versus MA0047.2 (Foxa2); m=1/6; ncol2=12; w=9; offset=6; strand=D; shift=6; score= 1.2857; ------TRTTTACwywgg ; cor=0.860; Ncor=0.430; logoDP=6.826; NIcor=0.417; NsEucl=0.913; SSD=1.223; NSW=0.932; rcor=1; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1 a 0 0 0 0 0 0 1 221 1 1 1 736 2 338 50 417 131 129 c 0 0 0 0 0 0 1 3 1 3 1 4 725 77 265 6 53 195 g 0 0 0 0 0 0 1 582 1 36 175 67 2 3 58 24 482 290 t 0 0 0 0 0 0 805 3 806 769 634 3 81 391 436 360 140 189

MA0047.1_shift3 (Foxa2) 0.791 0.633 6.095 0.599 0.909 2.373 0.901 2 1 4 1 2 6 2 2.571 2
; dyads_m2 versus MA0047.1 (Foxa2); m=2/6; ncol2=12; w=12; offset=3; strand=D; shift=3; score= 2.5714; ---mawTrTTkryTY--- ; cor=0.791; Ncor=0.633; logoDP=6.095; NIcor=0.599; NsEucl=0.909; SSD=2.373; NSW=0.901; rcor=2; rNcor=1; rlogoDP=4; rNIcor=1; rNsEucl=2; rSSD=6; rNSW=2; rank_mean=2.571; match_rank=2 a 0 0 0 6 11 8 0 11 0 0 0 9 0 1 0 0 0 0 c 0 0 0 7 3 3 1 0 1 1 0 0 9 1 5 0 0 0 g 0 0 0 3 1 1 0 6 0 0 6 8 0 1 0 0 0 0 t 0 0 0 1 2 5 16 0 16 16 11 0 8 14 12 0 0 0

MA0148.1_shift6 (FOXA1) 0.787 0.416 6.254 0.400 0.893 1.847 0.897 3 3 3 3 3 2 3 2.857 3
; dyads_m2 versus MA0148.1 (FOXA1); m=3/6; ncol2=11; w=9; offset=6; strand=D; shift=6; score= 2.8571; ------TGTTTrCwywg- ; cor=0.787; Ncor=0.416; logoDP=6.254; NIcor=0.400; NsEucl=0.893; SSD=1.847; NSW=0.897; rcor=3; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=2; rNSW=3; rank_mean=2.857; match_rank=3 a 0 0 0 0 0 0 13 108 1 5 6 476 6 291 45 378 90 0 c 0 0 0 0 0 0 2 7 7 7 3 12 807 106 368 9 125 0 g 0 0 0 0 0 0 2 770 5 24 78 368 5 5 69 24 466 0 t 0 0 0 0 0 0 875 8 882 860 809 40 79 495 414 482 211 0

MA0148.2_shift6 (FOXA1) 0.787 0.416 6.296 0.400 0.893 1.851 0.897 4 4 2 4 4 3 4 3.571 4
; dyads_m2 versus MA0148.2 (FOXA1); m=4/6; ncol2=11; w=9; offset=6; strand=D; shift=6; score= 3.5714; ------TGTTTrCwywg- ; cor=0.787; Ncor=0.416; logoDP=6.296; NIcor=0.400; NsEucl=0.893; SSD=1.851; NSW=0.897; rcor=4; rNcor=4; rlogoDP=2; rNIcor=4; rNsEucl=4; rSSD=3; rNSW=4; rank_mean=3.571; match_rank=4 a 0 0 0 0 0 0 13 108 1 4 6 478 4 289 42 379 89 0 c 0 0 0 0 0 0 1 7 7 7 3 12 808 106 369 7 125 0 g 0 0 0 0 0 0 2 772 4 24 77 368 5 5 69 24 467 0 t 0 0 0 0 0 0 876 7 885 862 811 38 79 496 414 482 211 0

MA0031.1_rc_shift5 (FOXD1_rc) 0.780 0.416 4.283 0.132 0.871 2.116 0.868 5 5 5 5 6 5 6 5.286 5
; dyads_m2 versus MA0031.1_rc (FOXD1_rc); m=5/6; ncol2=8; w=8; offset=5; strand=R; shift=5; score= 5.2857; -----wTGTTTAC----- ; cor=0.780; Ncor=0.416; logoDP=4.283; NIcor=0.132; NsEucl=0.871; SSD=2.116; NSW=0.868; rcor=5; rNcor=5; rlogoDP=5; rNIcor=5; rNsEucl=6; rSSD=5; rNSW=6; rank_mean=5.286; match_rank=5 a 0 0 0 0 0 8 0 1 0 0 0 20 1 0 0 0 0 0 c 0 0 0 0 0 3 0 0 1 0 0 0 17 0 0 0 0 0 g 0 0 0 0 0 2 0 18 1 0 1 0 1 0 0 0 0 0 t 0 0 0 0 0 7 20 1 18 20 19 0 1 0 0 0 0 0

MA0157.1_rc_shift6 (FOXO3_rc) 0.761 0.406 2.783 0.129 0.873 2.063 0.871 6 6 6 6 5 4 5 5.429 6
; dyads_m2 versus MA0157.1_rc (FOXO3_rc); m=6/6; ncol2=8; w=8; offset=6; strand=R; shift=6; score= 5.4286; ------TGTTTACm---- ; cor=0.761; Ncor=0.406; logoDP=2.783; NIcor=0.129; NsEucl=0.873; SSD=2.063; NSW=0.871; rcor=6; rNcor=6; rlogoDP=6; rNIcor=6; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=5.429; match_rank=6 a 0 0 0 0 0 0 1 1 0 0 0 9 0 8 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1 10 5 0 0 0 0 g 0 0 0 0 0 0 0 12 0 1 0 0 2 0 0 0 0 0 t 0 0 0 0 0 0 12 0 13 12 13 3 1 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m2_shift0 (dyads_m2)																	; dyads_m2; m=0 (reference); ncol1=15; shift=0; ncol=18; wrCAAATATTTACwt--- ; Alignment reference a 135 121 19 289 293 299 0 299 3 1 5 274 23 88 77 0 0 0 c 38 35 257 10 6 2 6 0 2 1 2 2 230 64 76 0 0 0 g 54 88 7 0 3 3 4 9 4 2 11 18 10 20 69 0 0 0 t 82 65 26 10 7 5 299 1 300 305 291 15 46 137 87 0 0 0
MA0047.2_shift6 (Foxa2)	0.860	0.430	6.826	0.417	0.913	1.223	0.932	1	2	1	2	1	1	1	1.286	1	; dyads_m2 versus MA0047.2 (Foxa2); m=1/6; ncol2=12; w=9; offset=6; strand=D; shift=6; score= 1.2857; ------TRTTTACwywgg ; cor=0.860; Ncor=0.430; logoDP=6.826; NIcor=0.417; NsEucl=0.913; SSD=1.223; NSW=0.932; rcor=1; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1 a 0 0 0 0 0 0 1 221 1 1 1 736 2 338 50 417 131 129 c 0 0 0 0 0 0 1 3 1 3 1 4 725 77 265 6 53 195 g 0 0 0 0 0 0 1 582 1 36 175 67 2 3 58 24 482 290 t 0 0 0 0 0 0 805 3 806 769 634 3 81 391 436 360 140 189
MA0047.1_shift3 (Foxa2)	0.791	0.633	6.095	0.599	0.909	2.373	0.901	2	1	4	1	2	6	2	2.571	2	; dyads_m2 versus MA0047.1 (Foxa2); m=2/6; ncol2=12; w=12; offset=3; strand=D; shift=3; score= 2.5714; ---mawTrTTkryTY--- ; cor=0.791; Ncor=0.633; logoDP=6.095; NIcor=0.599; NsEucl=0.909; SSD=2.373; NSW=0.901; rcor=2; rNcor=1; rlogoDP=4; rNIcor=1; rNsEucl=2; rSSD=6; rNSW=2; rank_mean=2.571; match_rank=2 a 0 0 0 6 11 8 0 11 0 0 0 9 0 1 0 0 0 0 c 0 0 0 7 3 3 1 0 1 1 0 0 9 1 5 0 0 0 g 0 0 0 3 1 1 0 6 0 0 6 8 0 1 0 0 0 0 t 0 0 0 1 2 5 16 0 16 16 11 0 8 14 12 0 0 0
MA0148.1_shift6 (FOXA1)	0.787	0.416	6.254	0.400	0.893	1.847	0.897	3	3	3	3	3	2	3	2.857	3	; dyads_m2 versus MA0148.1 (FOXA1); m=3/6; ncol2=11; w=9; offset=6; strand=D; shift=6; score= 2.8571; ------TGTTTrCwywg- ; cor=0.787; Ncor=0.416; logoDP=6.254; NIcor=0.400; NsEucl=0.893; SSD=1.847; NSW=0.897; rcor=3; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=2; rNSW=3; rank_mean=2.857; match_rank=3 a 0 0 0 0 0 0 13 108 1 5 6 476 6 291 45 378 90 0 c 0 0 0 0 0 0 2 7 7 7 3 12 807 106 368 9 125 0 g 0 0 0 0 0 0 2 770 5 24 78 368 5 5 69 24 466 0 t 0 0 0 0 0 0 875 8 882 860 809 40 79 495 414 482 211 0
MA0148.2_shift6 (FOXA1)	0.787	0.416	6.296	0.400	0.893	1.851	0.897	4	4	2	4	4	3	4	3.571	4	; dyads_m2 versus MA0148.2 (FOXA1); m=4/6; ncol2=11; w=9; offset=6; strand=D; shift=6; score= 3.5714; ------TGTTTrCwywg- ; cor=0.787; Ncor=0.416; logoDP=6.296; NIcor=0.400; NsEucl=0.893; SSD=1.851; NSW=0.897; rcor=4; rNcor=4; rlogoDP=2; rNIcor=4; rNsEucl=4; rSSD=3; rNSW=4; rank_mean=3.571; match_rank=4 a 0 0 0 0 0 0 13 108 1 4 6 478 4 289 42 379 89 0 c 0 0 0 0 0 0 1 7 7 7 3 12 808 106 369 7 125 0 g 0 0 0 0 0 0 2 772 4 24 77 368 5 5 69 24 467 0 t 0 0 0 0 0 0 876 7 885 862 811 38 79 496 414 482 211 0
MA0031.1_rc_shift5 (FOXD1_rc)	0.780	0.416	4.283	0.132	0.871	2.116	0.868	5	5	5	5	6	5	6	5.286	5	; dyads_m2 versus MA0031.1_rc (FOXD1_rc); m=5/6; ncol2=8; w=8; offset=5; strand=R; shift=5; score= 5.2857; -----wTGTTTAC----- ; cor=0.780; Ncor=0.416; logoDP=4.283; NIcor=0.132; NsEucl=0.871; SSD=2.116; NSW=0.868; rcor=5; rNcor=5; rlogoDP=5; rNIcor=5; rNsEucl=6; rSSD=5; rNSW=6; rank_mean=5.286; match_rank=5 a 0 0 0 0 0 8 0 1 0 0 0 20 1 0 0 0 0 0 c 0 0 0 0 0 3 0 0 1 0 0 0 17 0 0 0 0 0 g 0 0 0 0 0 2 0 18 1 0 1 0 1 0 0 0 0 0 t 0 0 0 0 0 7 20 1 18 20 19 0 1 0 0 0 0 0
MA0157.1_rc_shift6 (FOXO3_rc)	0.761	0.406	2.783	0.129	0.873	2.063	0.871	6	6	6	6	5	4	5	5.429	6	; dyads_m2 versus MA0157.1_rc (FOXO3_rc); m=6/6; ncol2=8; w=8; offset=6; strand=R; shift=6; score= 5.4286; ------TGTTTACm---- ; cor=0.761; Ncor=0.406; logoDP=2.783; NIcor=0.129; NsEucl=0.873; SSD=2.063; NSW=0.871; rcor=6; rNcor=6; rlogoDP=6; rNIcor=6; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=5.429; match_rank=6 a 0 0 0 0 0 0 1 1 0 0 0 9 0 8 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1 10 5 0 0 0 0 g 0 0 0 0 0 0 0 12 0 1 0 0 2 0 0 0 0 0 t 0 0 0 0 0 0 12 0 13 12 13 3 1 0 0 0 0 0