One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.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/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift1 ; 9 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
oligos_7nt_mkv5_m3_shift1 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=1; ncol=14; -wrTTACACAAya- ; Alignment reference a 0 701 1073 23 1 2580 0 2542 0 2578 2579 307 920 0 c 0 409 457 6 0 0 2580 0 2580 0 1 755 634 0 g 0 616 697 30 0 0 0 38 0 2 0 388 415 0 t 0 854 353 2521 2579 0 0 0 0 0 0 1130 611 0

MA0043.1_shift1 (HLF) 0.806 0.806 6.362 0.783 0.914 2.125 0.911 3 1 5 1 1 3 2 2.286 1
; oligos_7nt_mkv5_m3 versus MA0043.1 (HLF); m=1/8; ncol2=12; w=12; offset=0; strand=D; shift=1; score= 2.2857; -krTTACryAAth- ; cor=0.806; Ncor=0.806; logoDP=6.362; NIcor=0.783; NsEucl=0.914; SSD=2.125; NSW=0.911; rcor=3; rNcor=1; rlogoDP=5; rNIcor=1; rNsEucl=1; rSSD=3; rNSW=2; rank_mean=2.286; match_rank=1 a 0 1 6 1 0 13 0 6 0 13 15 2 5 0 c 0 4 0 0 0 1 15 0 9 4 0 3 5 0 g 0 8 12 0 3 2 1 12 0 1 1 1 3 0 t 0 5 0 17 15 2 2 0 9 0 2 12 5 0

MA0102.3_shift2 (CEBPA) 0.806 0.738 9.392 0.733 0.905 2.166 0.902 4 2 1 2 2 4 3 2.571 2
; oligos_7nt_mkv5_m3 versus MA0102.3 (CEBPA); m=2/8; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 2.5714; --aTTGCAyAAym- ; cor=0.806; Ncor=0.738; logoDP=9.392; NIcor=0.733; NsEucl=0.905; SSD=2.166; NSW=0.902; rcor=4; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=2; rSSD=4; rNSW=3; rank_mean=2.571; match_rank=2 a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0

MA0442.1_rc_shift7 (SOX10_rc) 0.842 0.421 0.061 -0.129 0.885 0.948 0.921 1 7 8 8 6 1 1 4.571 3
; oligos_7nt_mkv5_m3 versus MA0442.1_rc (SOX10_rc); m=3/8; ncol2=6; w=6; offset=6; strand=R; shift=7; score= 4.5714; -------ACAAwG- ; cor=0.842; Ncor=0.421; logoDP=0.061; NIcor=-0.129; NsEucl=0.885; SSD=0.948; NSW=0.921; rcor=1; rNcor=7; rlogoDP=8; rNIcor=8; rNsEucl=6; rSSD=1; rNSW=1; rank_mean=4.571; match_rank=3 a 0 0 0 0 0 0 0 21 0 22 17 10 3 0 c 0 0 0 0 0 0 0 1 19 0 4 2 0 0 g 0 0 0 0 0 0 0 0 3 0 1 2 19 0 t 0 0 0 0 0 0 0 0 0 0 0 8 0 0

MA0466.1_shift1 (CEBPB) 0.769 0.705 9.034 0.691 0.897 2.567 0.883 8 3 2 3 3 8 6 4.714 4
; oligos_7nt_mkv5_m3 versus MA0466.1 (CEBPB); m=4/8; ncol2=11; w=11; offset=0; strand=D; shift=1; score= 4.7143; -kATTGCAymAy-- ; cor=0.769; Ncor=0.705; logoDP=9.034; NIcor=0.691; NsEucl=0.897; SSD=2.567; NSW=0.883; rcor=8; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=3; rSSD=8; rNSW=6; rank_mean=4.714; match_rank=4 a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0

MA0078.1_rc_shift6 (Sox17_rc) 0.814 0.407 2.071 0.097 0.879 1.427 0.898 2 8 7 6 7 2 4 5.143 5
; oligos_7nt_mkv5_m3 versus MA0078.1_rc (Sox17_rc); m=5/8; ncol2=9; w=7; offset=5; strand=R; shift=6; score= 5.1429; ------sACAATrd ; cor=0.814; Ncor=0.407; logoDP=2.071; NIcor=0.097; NsEucl=0.879; SSD=1.427; NSW=0.898; rcor=2; rNcor=8; rlogoDP=7; rNIcor=6; rNsEucl=7; rSSD=2; rNSW=4; rank_mean=5.143; match_rank=5 a 0 0 0 0 0 0 4 29 0 31 30 1 9 11 c 0 0 0 0 0 0 10 2 31 0 0 0 1 4 g 0 0 0 0 0 0 17 0 0 0 1 0 18 8 t 0 0 0 0 0 0 0 0 0 0 0 30 3 8

MA0025.1_rc_shift0 (NFIL3_rc) 0.798 0.614 2.419 0.080 0.893 2.274 0.886 5 4 6 7 4 5 5 5.143 6
; oligos_7nt_mkv5_m3 versus MA0025.1_rc (NFIL3_rc); m=6/8; ncol2=11; w=10; offset=-1; strand=R; shift=0; score= 5.1429; ayrTTACrTAA--- ; cor=0.798; Ncor=0.614; logoDP=2.419; NIcor=0.080; NsEucl=0.893; SSD=2.274; NSW=0.886; rcor=5; rNcor=4; rlogoDP=6; rNIcor=7; rNsEucl=4; rSSD=5; rNSW=5; rank_mean=5.143; match_rank=6 a 10 4 8 0 0 23 0 15 1 21 22 0 0 0 c 3 7 4 1 0 0 21 0 0 2 0 0 0 0 g 5 5 11 0 0 0 0 8 0 0 0 0 0 0 t 5 7 0 22 23 0 2 0 22 0 1 0 0 0

MA0102.1_shift3 (Cebpa) 0.770 0.550 6.445 0.526 0.889 2.451 0.877 7 6 3 5 5 7 7 5.714 7
; oligos_7nt_mkv5_m3 versus MA0102.1 (Cebpa); m=7/8; ncol2=12; w=10; offset=2; strand=D; shift=3; score= 5.7143; ---TtkygCAAyvy ; cor=0.770; Ncor=0.550; logoDP=6.445; NIcor=0.526; NsEucl=0.889; SSD=2.451; NSW=0.877; rcor=7; rNcor=6; rlogoDP=3; rNIcor=5; rNsEucl=5; rSSD=7; rNSW=7; rank_mean=5.714; match_rank=7 a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 t 0 0 0 15 12 7 5 2 1 0 0 10 2 8

MA0102.2_shift3 (CEBPA) 0.775 0.581 6.445 0.550 0.878 2.408 0.866 6 5 4 4 8 6 8 5.857 8
; oligos_7nt_mkv5_m3 versus MA0102.2 (CEBPA); m=8/8; ncol2=9; w=9; offset=2; strand=D; shift=3; score= 5.8571; ---TtkygCAAy-- ; cor=0.775; Ncor=0.581; logoDP=6.445; NIcor=0.550; NsEucl=0.878; SSD=2.408; NSW=0.866; rcor=6; rNcor=5; rlogoDP=4; rNIcor=4; rNsEucl=8; rSSD=6; rNSW=8; rank_mean=5.857; match_rank=8 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m3_shift1 (oligos_7nt_mkv5_m3)																	; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=1; ncol=14; -wrTTACACAAya- ; Alignment reference a 0 701 1073 23 1 2580 0 2542 0 2578 2579 307 920 0 c 0 409 457 6 0 0 2580 0 2580 0 1 755 634 0 g 0 616 697 30 0 0 0 38 0 2 0 388 415 0 t 0 854 353 2521 2579 0 0 0 0 0 0 1130 611 0
MA0043.1_shift1 (HLF)	0.806	0.806	6.362	0.783	0.914	2.125	0.911	3	1	5	1	1	3	2	2.286	1	; oligos_7nt_mkv5_m3 versus MA0043.1 (HLF); m=1/8; ncol2=12; w=12; offset=0; strand=D; shift=1; score= 2.2857; -krTTACryAAth- ; cor=0.806; Ncor=0.806; logoDP=6.362; NIcor=0.783; NsEucl=0.914; SSD=2.125; NSW=0.911; rcor=3; rNcor=1; rlogoDP=5; rNIcor=1; rNsEucl=1; rSSD=3; rNSW=2; rank_mean=2.286; match_rank=1 a 0 1 6 1 0 13 0 6 0 13 15 2 5 0 c 0 4 0 0 0 1 15 0 9 4 0 3 5 0 g 0 8 12 0 3 2 1 12 0 1 1 1 3 0 t 0 5 0 17 15 2 2 0 9 0 2 12 5 0
MA0102.3_shift2 (CEBPA)	0.806	0.738	9.392	0.733	0.905	2.166	0.902	4	2	1	2	2	4	3	2.571	2	; oligos_7nt_mkv5_m3 versus MA0102.3 (CEBPA); m=2/8; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 2.5714; --aTTGCAyAAym- ; cor=0.806; Ncor=0.738; logoDP=9.392; NIcor=0.733; NsEucl=0.905; SSD=2.166; NSW=0.902; rcor=4; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=2; rSSD=4; rNSW=3; rank_mean=2.571; match_rank=2 a 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0442.1_rc_shift7 (SOX10_rc)	0.842	0.421	0.061	-0.129	0.885	0.948	0.921	1	7	8	8	6	1	1	4.571	3	; oligos_7nt_mkv5_m3 versus MA0442.1_rc (SOX10_rc); m=3/8; ncol2=6; w=6; offset=6; strand=R; shift=7; score= 4.5714; -------ACAAwG- ; cor=0.842; Ncor=0.421; logoDP=0.061; NIcor=-0.129; NsEucl=0.885; SSD=0.948; NSW=0.921; rcor=1; rNcor=7; rlogoDP=8; rNIcor=8; rNsEucl=6; rSSD=1; rNSW=1; rank_mean=4.571; match_rank=3 a 0 0 0 0 0 0 0 21 0 22 17 10 3 0 c 0 0 0 0 0 0 0 1 19 0 4 2 0 0 g 0 0 0 0 0 0 0 0 3 0 1 2 19 0 t 0 0 0 0 0 0 0 0 0 0 0 8 0 0
MA0466.1_shift1 (CEBPB)	0.769	0.705	9.034	0.691	0.897	2.567	0.883	8	3	2	3	3	8	6	4.714	4	; oligos_7nt_mkv5_m3 versus MA0466.1 (CEBPB); m=4/8; ncol2=11; w=11; offset=0; strand=D; shift=1; score= 4.7143; -kATTGCAymAy-- ; cor=0.769; Ncor=0.705; logoDP=9.034; NIcor=0.691; NsEucl=0.897; SSD=2.567; NSW=0.883; rcor=8; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=3; rSSD=8; rNSW=6; rank_mean=4.714; match_rank=4 a 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0078.1_rc_shift6 (Sox17_rc)	0.814	0.407	2.071	0.097	0.879	1.427	0.898	2	8	7	6	7	2	4	5.143	5	; oligos_7nt_mkv5_m3 versus MA0078.1_rc (Sox17_rc); m=5/8; ncol2=9; w=7; offset=5; strand=R; shift=6; score= 5.1429; ------sACAATrd ; cor=0.814; Ncor=0.407; logoDP=2.071; NIcor=0.097; NsEucl=0.879; SSD=1.427; NSW=0.898; rcor=2; rNcor=8; rlogoDP=7; rNIcor=6; rNsEucl=7; rSSD=2; rNSW=4; rank_mean=5.143; match_rank=5 a 0 0 0 0 0 0 4 29 0 31 30 1 9 11 c 0 0 0 0 0 0 10 2 31 0 0 0 1 4 g 0 0 0 0 0 0 17 0 0 0 1 0 18 8 t 0 0 0 0 0 0 0 0 0 0 0 30 3 8
MA0025.1_rc_shift0 (NFIL3_rc)	0.798	0.614	2.419	0.080	0.893	2.274	0.886	5	4	6	7	4	5	5	5.143	6	; oligos_7nt_mkv5_m3 versus MA0025.1_rc (NFIL3_rc); m=6/8; ncol2=11; w=10; offset=-1; strand=R; shift=0; score= 5.1429; ayrTTACrTAA--- ; cor=0.798; Ncor=0.614; logoDP=2.419; NIcor=0.080; NsEucl=0.893; SSD=2.274; NSW=0.886; rcor=5; rNcor=4; rlogoDP=6; rNIcor=7; rNsEucl=4; rSSD=5; rNSW=5; rank_mean=5.143; match_rank=6 a 10 4 8 0 0 23 0 15 1 21 22 0 0 0 c 3 7 4 1 0 0 21 0 0 2 0 0 0 0 g 5 5 11 0 0 0 0 8 0 0 0 0 0 0 t 5 7 0 22 23 0 2 0 22 0 1 0 0 0
MA0102.1_shift3 (Cebpa)	0.770	0.550	6.445	0.526	0.889	2.451	0.877	7	6	3	5	5	7	7	5.714	7	; oligos_7nt_mkv5_m3 versus MA0102.1 (Cebpa); m=7/8; ncol2=12; w=10; offset=2; strand=D; shift=3; score= 5.7143; ---TtkygCAAyvy ; cor=0.770; Ncor=0.550; logoDP=6.445; NIcor=0.526; NsEucl=0.889; SSD=2.451; NSW=0.877; rcor=7; rNcor=6; rlogoDP=3; rNIcor=5; rNsEucl=5; rSSD=7; rNSW=7; rank_mean=5.714; match_rank=7 a 0 0 0 3 1 4 2 4 2 18 18 0 5 2 c 0 0 0 0 1 1 9 2 15 0 0 6 6 5 g 0 0 0 0 4 6 2 10 0 0 0 2 5 3 t 0 0 0 15 12 7 5 2 1 0 0 10 2 8
MA0102.2_shift3 (CEBPA)	0.775	0.581	6.445	0.550	0.878	2.408	0.866	6	5	4	4	8	6	8	5.857	8	; oligos_7nt_mkv5_m3 versus MA0102.2 (CEBPA); m=8/8; ncol2=9; w=9; offset=2; strand=D; shift=3; score= 5.8571; ---TtkygCAAy-- ; cor=0.775; Ncor=0.581; logoDP=6.445; NIcor=0.550; NsEucl=0.878; SSD=2.408; NSW=0.866; rcor=6; rNcor=5; rlogoDP=4; rNIcor=4; rNsEucl=8; rSSD=6; rNSW=8; rank_mean=5.857; match_rank=8 a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 t 0 0 0 15 12 7 5 2 1 0 0 10 0 0