One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/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.2014-09-03.094519_2014-09-03.094519_gM9GBj/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 ; 8 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=13; shift=1; ncol=14; -wrTTACACAAtww ; Alignment reference a 0 858 1227 211 1 2938 0 2923 0 2923 2926 729 1021 848 c 0 454 523 61 1 0 2937 0 2935 0 3 720 718 708 g 0 669 744 112 0 0 0 15 0 13 3 388 442 590 t 0 957 444 2554 2936 0 1 0 3 2 6 1101 757 792

MA0043.1_shift1 (HLF) 0.788 0.727 5.794 0.702 0.912 2.217 0.908 4 1 4 1 1 3 2 2.286 1
; oligos_7nt_mkv5_m3 versus MA0043.1 (HLF); m=1/7; ncol2=12; w=12; offset=0; strand=D; shift=1; score= 2.2857; -krTTACryAAth- ; cor=0.788; Ncor=0.727; logoDP=5.794; NIcor=0.702; NsEucl=0.912; SSD=2.217; NSW=0.908; rcor=4; rNcor=1; rlogoDP=4; 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) 0.790 0.669 8.675 0.664 0.903 2.262 0.897 2 2 1 2 2 4 4 2.429 2
; oligos_7nt_mkv5_m3 versus MA0102.3 (CEBPA); m=2/7; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 2.4286; --aTTGCAyAAym- ; cor=0.790; Ncor=0.669; logoDP=8.675; NIcor=0.664; NsEucl=0.903; SSD=2.262; NSW=0.897; rcor=2; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=2; rSSD=4; rNSW=4; rank_mean=2.429; 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

MA0078.1_rc_shift6 (Sox17_rc) 0.799 0.456 1.990 0.086 0.890 1.541 0.904 1 6 7 6 5 2 3 4.286 3
; oligos_7nt_mkv5_m3 versus MA0078.1_rc (Sox17_rc); m=3/7; ncol2=9; w=8; offset=5; strand=R; shift=6; score= 4.2857; ------sACAATrd ; cor=0.799; Ncor=0.456; logoDP=1.990; NIcor=0.086; NsEucl=0.890; SSD=1.541; NSW=0.904; rcor=1; rNcor=6; rlogoDP=7; rNIcor=6; rNsEucl=5; rSSD=2; rNSW=3; rank_mean=4.286; match_rank=3 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

MA0133.1_shift7 (BRCA1) 0.779 0.419 3.209 0.421 0.890 1.196 0.915 5 7 5 5 6 1 1 4.286 4
; oligos_7nt_mkv5_m3 versus MA0133.1 (BRCA1); m=4/7; ncol2=7; w=7; offset=6; strand=D; shift=7; score= 4.2857; -------mCAAcms ; cor=0.779; Ncor=0.419; logoDP=3.209; NIcor=0.421; NsEucl=0.890; SSD=1.196; NSW=0.915; rcor=5; rNcor=7; rlogoDP=5; rNIcor=5; rNsEucl=6; rSSD=1; rNSW=1; rank_mean=4.286; match_rank=4 a 0 0 0 0 0 0 0 15 4 41 36 7 19 3 c 0 0 0 0 0 0 0 11 35 1 2 29 14 22 g 0 0 0 0 0 0 0 10 2 1 4 6 7 15 t 0 0 0 0 0 0 0 7 2 0 1 1 3 3

MA0466.1_shift1 (CEBPB) 0.752 0.636 8.314 0.623 0.895 2.680 0.878 7 3 2 3 3 7 6 4.429 5
; oligos_7nt_mkv5_m3 versus MA0466.1 (CEBPB); m=5/7; ncol2=11; w=11; offset=0; strand=D; shift=1; score= 4.4286; -kATTGCAymAy-- ; cor=0.752; Ncor=0.636; logoDP=8.314; NIcor=0.623; NsEucl=0.895; SSD=2.680; NSW=0.878; rcor=7; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=3; rSSD=7; rNSW=6; rank_mean=4.429; match_rank=5 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

MA0025.1_rc_shift0 (NFIL3_rc) 0.790 0.564 2.256 0.072 0.893 2.310 0.884 3 4 6 7 4 5 5 4.857 6
; oligos_7nt_mkv5_m3 versus MA0025.1_rc (NFIL3_rc); m=6/7; ncol2=11; w=10; offset=-1; strand=R; shift=0; score= 4.8571; ayrTTACrTAA--- ; cor=0.790; Ncor=0.564; logoDP=2.256; NIcor=0.072; NsEucl=0.893; SSD=2.310; NSW=0.884; rcor=3; rNcor=4; rlogoDP=6; rNIcor=7; rNsEucl=4; rSSD=5; rNSW=5; rank_mean=4.857; 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

MA0102.2_shift3 (CEBPA) 0.756 0.523 5.976 0.496 0.877 2.470 0.863 6 5 3 4 7 6 7 5.429 7
; oligos_7nt_mkv5_m3 versus MA0102.2 (CEBPA); m=7/7; ncol2=9; w=9; offset=2; strand=D; shift=3; score= 5.4286; ---TtkygCAAy-- ; cor=0.756; Ncor=0.523; logoDP=5.976; NIcor=0.496; NsEucl=0.877; SSD=2.470; NSW=0.863; rcor=6; rNcor=5; rlogoDP=3; rNIcor=4; rNsEucl=7; rSSD=6; rNSW=7; rank_mean=5.429; match_rank=7 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=13; shift=1; ncol=14; -wrTTACACAAtww ; Alignment reference a 0 858 1227 211 1 2938 0 2923 0 2923 2926 729 1021 848 c 0 454 523 61 1 0 2937 0 2935 0 3 720 718 708 g 0 669 744 112 0 0 0 15 0 13 3 388 442 590 t 0 957 444 2554 2936 0 1 0 3 2 6 1101 757 792
MA0043.1_shift1 (HLF)	0.788	0.727	5.794	0.702	0.912	2.217	0.908	4	1	4	1	1	3	2	2.286	1	; oligos_7nt_mkv5_m3 versus MA0043.1 (HLF); m=1/7; ncol2=12; w=12; offset=0; strand=D; shift=1; score= 2.2857; -krTTACryAAth- ; cor=0.788; Ncor=0.727; logoDP=5.794; NIcor=0.702; NsEucl=0.912; SSD=2.217; NSW=0.908; rcor=4; rNcor=1; rlogoDP=4; 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)	0.790	0.669	8.675	0.664	0.903	2.262	0.897	2	2	1	2	2	4	4	2.429	2	; oligos_7nt_mkv5_m3 versus MA0102.3 (CEBPA); m=2/7; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 2.4286; --aTTGCAyAAym- ; cor=0.790; Ncor=0.669; logoDP=8.675; NIcor=0.664; NsEucl=0.903; SSD=2.262; NSW=0.897; rcor=2; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=2; rSSD=4; rNSW=4; rank_mean=2.429; 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
MA0078.1_rc_shift6 (Sox17_rc)	0.799	0.456	1.990	0.086	0.890	1.541	0.904	1	6	7	6	5	2	3	4.286	3	; oligos_7nt_mkv5_m3 versus MA0078.1_rc (Sox17_rc); m=3/7; ncol2=9; w=8; offset=5; strand=R; shift=6; score= 4.2857; ------sACAATrd ; cor=0.799; Ncor=0.456; logoDP=1.990; NIcor=0.086; NsEucl=0.890; SSD=1.541; NSW=0.904; rcor=1; rNcor=6; rlogoDP=7; rNIcor=6; rNsEucl=5; rSSD=2; rNSW=3; rank_mean=4.286; match_rank=3 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
MA0133.1_shift7 (BRCA1)	0.779	0.419	3.209	0.421	0.890	1.196	0.915	5	7	5	5	6	1	1	4.286	4	; oligos_7nt_mkv5_m3 versus MA0133.1 (BRCA1); m=4/7; ncol2=7; w=7; offset=6; strand=D; shift=7; score= 4.2857; -------mCAAcms ; cor=0.779; Ncor=0.419; logoDP=3.209; NIcor=0.421; NsEucl=0.890; SSD=1.196; NSW=0.915; rcor=5; rNcor=7; rlogoDP=5; rNIcor=5; rNsEucl=6; rSSD=1; rNSW=1; rank_mean=4.286; match_rank=4 a 0 0 0 0 0 0 0 15 4 41 36 7 19 3 c 0 0 0 0 0 0 0 11 35 1 2 29 14 22 g 0 0 0 0 0 0 0 10 2 1 4 6 7 15 t 0 0 0 0 0 0 0 7 2 0 1 1 3 3
MA0466.1_shift1 (CEBPB)	0.752	0.636	8.314	0.623	0.895	2.680	0.878	7	3	2	3	3	7	6	4.429	5	; oligos_7nt_mkv5_m3 versus MA0466.1 (CEBPB); m=5/7; ncol2=11; w=11; offset=0; strand=D; shift=1; score= 4.4286; -kATTGCAymAy-- ; cor=0.752; Ncor=0.636; logoDP=8.314; NIcor=0.623; NsEucl=0.895; SSD=2.680; NSW=0.878; rcor=7; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=3; rSSD=7; rNSW=6; rank_mean=4.429; match_rank=5 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
MA0025.1_rc_shift0 (NFIL3_rc)	0.790	0.564	2.256	0.072	0.893	2.310	0.884	3	4	6	7	4	5	5	4.857	6	; oligos_7nt_mkv5_m3 versus MA0025.1_rc (NFIL3_rc); m=6/7; ncol2=11; w=10; offset=-1; strand=R; shift=0; score= 4.8571; ayrTTACrTAA--- ; cor=0.790; Ncor=0.564; logoDP=2.256; NIcor=0.072; NsEucl=0.893; SSD=2.310; NSW=0.884; rcor=3; rNcor=4; rlogoDP=6; rNIcor=7; rNsEucl=4; rSSD=5; rNSW=5; rank_mean=4.857; 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
MA0102.2_shift3 (CEBPA)	0.756	0.523	5.976	0.496	0.877	2.470	0.863	6	5	3	4	7	6	7	5.429	7	; oligos_7nt_mkv5_m3 versus MA0102.2 (CEBPA); m=7/7; ncol2=9; w=9; offset=2; strand=D; shift=3; score= 5.4286; ---TtkygCAAy-- ; cor=0.756; Ncor=0.523; logoDP=5.976; NIcor=0.496; NsEucl=0.877; SSD=2.470; NSW=0.863; rcor=6; rNcor=5; rlogoDP=3; rNIcor=4; rNsEucl=7; rSSD=6; rNSW=7; rank_mean=5.429; match_rank=7 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