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_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4.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_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m4_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_8nt_mkv6_m4_shift1 (oligos_8nt_mkv6_m4)
; oligos_8nt_mkv6_m4; m=0 (reference); ncol1=13; shift=1; ncol=14; -wrTTACACAATah ; Alignment reference a 0 768 1278 9 3 2545 2 2026 1 2529 2545 143 934 674 c 0 372 377 3 0 0 2552 7 2516 4 1 447 595 648 g 0 562 670 8 10 10 2 516 0 21 8 179 403 433 t 0 862 239 2544 2551 9 8 15 47 10 10 1795 632 809

MA0043.1_shift1 (HLF) 0.856 0.791 6.300 0.768 0.925 1.604 0.933 1 1 3 1 1 2 1 1.429 1
; oligos_8nt_mkv6_m4 versus MA0043.1 (HLF); m=1/7; ncol2=12; w=12; offset=0; strand=D; shift=1; score= 1.4286; -krTTACryAAth- ; cor=0.856; Ncor=0.791; logoDP=6.300; NIcor=0.768; NsEucl=0.925; SSD=1.604; NSW=0.933; rcor=1; rNcor=1; rlogoDP=3; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.429; 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) 0.810 0.686 9.050 0.681 0.907 2.083 0.905 5 2 1 2 3 6 4 3.286 2
; oligos_8nt_mkv6_m4 versus MA0102.3 (CEBPA); m=2/7; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 3.2857; --aTTGCAyAAym- ; cor=0.810; Ncor=0.686; logoDP=9.050; NIcor=0.681; NsEucl=0.907; SSD=2.083; NSW=0.905; rcor=5; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=3; rSSD=6; rNSW=4; rank_mean=3.286; 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

MA0102.1_shift3 (Cebpa) 0.807 0.634 6.278 0.610 0.908 2.061 0.906 6 4 4 4 2 5 3 4.000 3
; oligos_8nt_mkv6_m4 versus MA0102.1 (Cebpa); m=3/7; ncol2=12; w=11; offset=2; strand=D; shift=3; score= 4; ---TtkygCAAyvy ; cor=0.807; Ncor=0.634; logoDP=6.278; NIcor=0.610; NsEucl=0.908; SSD=2.061; NSW=0.906; rcor=6; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=2; rSSD=5; rNSW=3; rank_mean=4.000; match_rank=3 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

MA0078.1_rc_shift6 (Sox17_rc) 0.837 0.479 2.335 0.155 0.902 1.226 0.923 2 7 6 6 4 1 2 4.000 4
; oligos_8nt_mkv6_m4 versus MA0078.1_rc (Sox17_rc); m=4/7; ncol2=9; w=8; offset=5; strand=R; shift=6; score= 4; ------sACAATrd ; cor=0.837; Ncor=0.479; logoDP=2.335; NIcor=0.155; NsEucl=0.902; SSD=1.226; NSW=0.923; rcor=2; rNcor=7; rlogoDP=6; rNIcor=6; rNsEucl=4; rSSD=1; rNSW=2; rank_mean=4.000; match_rank=4 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

MA0466.1_shift1 (CEBPB) 0.784 0.663 8.817 0.653 0.901 2.373 0.892 7 3 2 3 5 7 6 4.714 5
; oligos_8nt_mkv6_m4 versus MA0466.1 (CEBPB); m=5/7; ncol2=11; w=11; offset=0; strand=D; shift=1; score= 4.7143; -kATTGCAymAy-- ; cor=0.784; Ncor=0.663; logoDP=8.817; NIcor=0.653; NsEucl=0.901; SSD=2.373; NSW=0.892; rcor=7; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=5; rSSD=7; rNSW=6; rank_mean=4.714; 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

MA0102.2_shift3 (CEBPA) 0.817 0.566 6.276 0.537 0.890 1.970 0.891 3 6 5 5 7 3 7 5.143 6
; oligos_8nt_mkv6_m4 versus MA0102.2 (CEBPA); m=6/7; ncol2=9; w=9; offset=2; strand=D; shift=3; score= 5.1429; ---TtkygCAAy-- ; cor=0.817; Ncor=0.566; logoDP=6.276; NIcor=0.537; NsEucl=0.890; SSD=1.970; NSW=0.891; rcor=3; rNcor=6; rlogoDP=5; rNIcor=5; rNsEucl=7; rSSD=3; rNSW=7; rank_mean=5.143; match_rank=6 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

MA0025.1_rc_shift0 (NFIL3_rc) 0.812 0.580 1.804 0.055 0.899 2.039 0.898 4 5 7 7 6 4 5 5.429 7
; oligos_8nt_mkv6_m4 versus MA0025.1_rc (NFIL3_rc); m=7/7; ncol2=11; w=10; offset=-1; strand=R; shift=0; score= 5.4286; ayrTTACrTAA--- ; cor=0.812; Ncor=0.580; logoDP=1.804; NIcor=0.055; NsEucl=0.899; SSD=2.039; NSW=0.898; rcor=4; rNcor=5; rlogoDP=7; rNIcor=7; rNsEucl=6; rSSD=4; rNSW=5; rank_mean=5.429; match_rank=7 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

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_8nt_mkv6_m4_shift1 (oligos_8nt_mkv6_m4)																	; oligos_8nt_mkv6_m4; m=0 (reference); ncol1=13; shift=1; ncol=14; -wrTTACACAATah ; Alignment reference a 0 768 1278 9 3 2545 2 2026 1 2529 2545 143 934 674 c 0 372 377 3 0 0 2552 7 2516 4 1 447 595 648 g 0 562 670 8 10 10 2 516 0 21 8 179 403 433 t 0 862 239 2544 2551 9 8 15 47 10 10 1795 632 809
MA0043.1_shift1 (HLF)	0.856	0.791	6.300	0.768	0.925	1.604	0.933	1	1	3	1	1	2	1	1.429	1	; oligos_8nt_mkv6_m4 versus MA0043.1 (HLF); m=1/7; ncol2=12; w=12; offset=0; strand=D; shift=1; score= 1.4286; -krTTACryAAth- ; cor=0.856; Ncor=0.791; logoDP=6.300; NIcor=0.768; NsEucl=0.925; SSD=1.604; NSW=0.933; rcor=1; rNcor=1; rlogoDP=3; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.429; 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)	0.810	0.686	9.050	0.681	0.907	2.083	0.905	5	2	1	2	3	6	4	3.286	2	; oligos_8nt_mkv6_m4 versus MA0102.3 (CEBPA); m=2/7; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 3.2857; --aTTGCAyAAym- ; cor=0.810; Ncor=0.686; logoDP=9.050; NIcor=0.681; NsEucl=0.907; SSD=2.083; NSW=0.905; rcor=5; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=3; rSSD=6; rNSW=4; rank_mean=3.286; 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
MA0102.1_shift3 (Cebpa)	0.807	0.634	6.278	0.610	0.908	2.061	0.906	6	4	4	4	2	5	3	4.000	3	; oligos_8nt_mkv6_m4 versus MA0102.1 (Cebpa); m=3/7; ncol2=12; w=11; offset=2; strand=D; shift=3; score= 4; ---TtkygCAAyvy ; cor=0.807; Ncor=0.634; logoDP=6.278; NIcor=0.610; NsEucl=0.908; SSD=2.061; NSW=0.906; rcor=6; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=2; rSSD=5; rNSW=3; rank_mean=4.000; match_rank=3 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
MA0078.1_rc_shift6 (Sox17_rc)	0.837	0.479	2.335	0.155	0.902	1.226	0.923	2	7	6	6	4	1	2	4.000	4	; oligos_8nt_mkv6_m4 versus MA0078.1_rc (Sox17_rc); m=4/7; ncol2=9; w=8; offset=5; strand=R; shift=6; score= 4; ------sACAATrd ; cor=0.837; Ncor=0.479; logoDP=2.335; NIcor=0.155; NsEucl=0.902; SSD=1.226; NSW=0.923; rcor=2; rNcor=7; rlogoDP=6; rNIcor=6; rNsEucl=4; rSSD=1; rNSW=2; rank_mean=4.000; match_rank=4 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
MA0466.1_shift1 (CEBPB)	0.784	0.663	8.817	0.653	0.901	2.373	0.892	7	3	2	3	5	7	6	4.714	5	; oligos_8nt_mkv6_m4 versus MA0466.1 (CEBPB); m=5/7; ncol2=11; w=11; offset=0; strand=D; shift=1; score= 4.7143; -kATTGCAymAy-- ; cor=0.784; Ncor=0.663; logoDP=8.817; NIcor=0.653; NsEucl=0.901; SSD=2.373; NSW=0.892; rcor=7; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=5; rSSD=7; rNSW=6; rank_mean=4.714; 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
MA0102.2_shift3 (CEBPA)	0.817	0.566	6.276	0.537	0.890	1.970	0.891	3	6	5	5	7	3	7	5.143	6	; oligos_8nt_mkv6_m4 versus MA0102.2 (CEBPA); m=6/7; ncol2=9; w=9; offset=2; strand=D; shift=3; score= 5.1429; ---TtkygCAAy-- ; cor=0.817; Ncor=0.566; logoDP=6.276; NIcor=0.537; NsEucl=0.890; SSD=1.970; NSW=0.891; rcor=3; rNcor=6; rlogoDP=5; rNIcor=5; rNsEucl=7; rSSD=3; rNSW=7; rank_mean=5.143; match_rank=6 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
MA0025.1_rc_shift0 (NFIL3_rc)	0.812	0.580	1.804	0.055	0.899	2.039	0.898	4	5	7	7	6	4	5	5.429	7	; oligos_8nt_mkv6_m4 versus MA0025.1_rc (NFIL3_rc); m=7/7; ncol2=11; w=10; offset=-1; strand=R; shift=0; score= 5.4286; ayrTTACrTAA--- ; cor=0.812; Ncor=0.580; logoDP=1.804; NIcor=0.055; NsEucl=0.899; SSD=2.039; NSW=0.898; rcor=4; rNcor=5; rlogoDP=7; rNIcor=7; rNsEucl=6; rSSD=4; rNSW=5; rank_mean=5.429; match_rank=7 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