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_m1/peak-motifs_oligos_7nt_mkv5_m1.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_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift1 ; 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
oligos_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=15; shift=1; ncol=16; -wkATTGCACAATcwy ; Alignment reference a 0 881 596 2604 4 6 132 4 2769 41 2931 2943 37 506 1027 722 c 0 545 555 127 12 0 10 2960 44 2728 35 5 195 1897 703 784 g 0 620 810 181 8 12 2652 3 37 10 2 12 67 243 299 499 t 0 926 1011 60 2948 2954 178 5 122 193 4 12 2673 326 943 967

MA0466.1_shift2 (CEBPB) 0.934 0.685 9.857 0.677 0.940 0.865 0.961 2 2 2 1 1 1 1 1.429 1
; oligos_7nt_mkv5_m1 versus MA0466.1 (CEBPB); m=1/6; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 1.4286; --kATTGCAymAy--- ; cor=0.934; Ncor=0.685; logoDP=9.857; NIcor=0.677; NsEucl=0.940; SSD=0.865; NSW=0.961; rcor=2; rNcor=2; rlogoDP=2; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.429; match_rank=1 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0

MA0102.3_shift3 (CEBPA) 0.935 0.685 9.923 0.674 0.939 0.907 0.959 1 1 1 2 2 2 2 1.571 2
; oligos_7nt_mkv5_m1 versus MA0102.3 (CEBPA); m=2/6; ncol2=11; w=11; offset=2; strand=D; shift=3; score= 1.5714; ---aTTGCAyAAym-- ; cor=0.935; Ncor=0.685; logoDP=9.923; NIcor=0.674; NsEucl=0.939; SSD=0.907; NSW=0.959; rcor=1; rNcor=1; rlogoDP=1; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.571; match_rank=2 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0

MA0102.1_shift4 (Cebpa) 0.797 0.637 6.191 0.620 0.910 2.314 0.904 5 3 3 3 3 5 4 3.714 3
; oligos_7nt_mkv5_m1 versus MA0102.1 (Cebpa); m=3/6; ncol2=12; w=12; offset=3; strand=D; shift=4; score= 3.7143; ----TtkygCAAyvyb ; cor=0.797; Ncor=0.637; logoDP=6.191; NIcor=0.620; NsEucl=0.910; SSD=2.314; NSW=0.904; rcor=5; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=5; rNSW=4; rank_mean=3.714; match_rank=3 a 0 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6

MA0078.1_rc_shift7 (Sox17_rc) 0.816 0.490 3.080 0.177 0.904 1.499 0.917 4 6 4 4 4 3 3 4.000 4
; oligos_7nt_mkv5_m1 versus MA0078.1_rc (Sox17_rc); m=4/6; ncol2=9; w=9; offset=6; strand=R; shift=7; score= 4; -------sACAATrdr ; cor=0.816; Ncor=0.490; logoDP=3.080; NIcor=0.177; NsEucl=0.904; SSD=1.499; NSW=0.917; rcor=4; rNcor=6; rlogoDP=4; rNIcor=4; rNsEucl=4; rSSD=3; rNSW=3; rank_mean=4.000; match_rank=4 a 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 c 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 g 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 t 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7

MA0102.2_rc_shift3 (CEBPA_rc) 0.838 0.503 2.596 0.048 0.893 1.848 0.897 3 5 5 5 6 4 5 4.714 5
; oligos_7nt_mkv5_m1 versus MA0102.2_rc (CEBPA_rc); m=5/6; ncol2=9; w=9; offset=2; strand=R; shift=3; score= 4.7143; ---rTTGcrmaA---- ; cor=0.838; Ncor=0.503; logoDP=2.596; NIcor=0.048; NsEucl=0.893; SSD=1.848; NSW=0.897; rcor=3; rNcor=5; rlogoDP=5; rNIcor=5; rNsEucl=6; rSSD=4; rNSW=5; rank_mean=4.714; match_rank=5 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0 0

MA0019.1_rc_shift0 (Ddit3::Cebpa_rc) 0.756 0.520 0.428 -0.161 0.896 2.597 0.882 6 4 6 6 5 6 6 5.571 6
; oligos_7nt_mkv5_m1 versus MA0019.1_rc (Ddit3::Cebpa_rc); m=6/6; ncol2=12; w=11; offset=-1; strand=R; shift=0; score= 5.5714; ggkATTGCAyyy---- ; cor=0.756; Ncor=0.520; logoDP=0.428; NIcor=-0.161; NsEucl=0.896; SSD=2.597; NSW=0.882; rcor=6; rNcor=4; rlogoDP=6; rNIcor=6; rNsEucl=5; rSSD=6; rNSW=6; rank_mean=5.571; match_rank=6 a 7 3 3 33 0 0 2 1 38 3 7 6 0 0 0 0 c 6 9 5 0 1 0 0 38 0 15 14 12 0 0 0 0 g 26 23 17 6 2 1 33 0 1 3 7 7 0 0 0 0 t 0 4 14 0 36 38 4 0 0 18 11 14 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
oligos_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1)																	; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=15; shift=1; ncol=16; -wkATTGCACAATcwy ; Alignment reference a 0 881 596 2604 4 6 132 4 2769 41 2931 2943 37 506 1027 722 c 0 545 555 127 12 0 10 2960 44 2728 35 5 195 1897 703 784 g 0 620 810 181 8 12 2652 3 37 10 2 12 67 243 299 499 t 0 926 1011 60 2948 2954 178 5 122 193 4 12 2673 326 943 967
MA0466.1_shift2 (CEBPB)	0.934	0.685	9.857	0.677	0.940	0.865	0.961	2	2	2	1	1	1	1	1.429	1	; oligos_7nt_mkv5_m1 versus MA0466.1 (CEBPB); m=1/6; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 1.4286; --kATTGCAymAy--- ; cor=0.934; Ncor=0.685; logoDP=9.857; NIcor=0.677; NsEucl=0.940; SSD=0.865; NSW=0.961; rcor=2; rNcor=2; rlogoDP=2; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.429; match_rank=1 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
MA0102.3_shift3 (CEBPA)	0.935	0.685	9.923	0.674	0.939	0.907	0.959	1	1	1	2	2	2	2	1.571	2	; oligos_7nt_mkv5_m1 versus MA0102.3 (CEBPA); m=2/6; ncol2=11; w=11; offset=2; strand=D; shift=3; score= 1.5714; ---aTTGCAyAAym-- ; cor=0.935; Ncor=0.685; logoDP=9.923; NIcor=0.674; NsEucl=0.939; SSD=0.907; NSW=0.959; rcor=1; rNcor=1; rlogoDP=1; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.571; match_rank=2 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
MA0102.1_shift4 (Cebpa)	0.797	0.637	6.191	0.620	0.910	2.314	0.904	5	3	3	3	3	5	4	3.714	3	; oligos_7nt_mkv5_m1 versus MA0102.1 (Cebpa); m=3/6; ncol2=12; w=12; offset=3; strand=D; shift=4; score= 3.7143; ----TtkygCAAyvyb ; cor=0.797; Ncor=0.637; logoDP=6.191; NIcor=0.620; NsEucl=0.910; SSD=2.314; NSW=0.904; rcor=5; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=5; rNSW=4; rank_mean=3.714; match_rank=3 a 0 0 0 0 3 1 4 2 4 2 18 18 0 5 2 1 c 0 0 0 0 0 1 1 9 2 15 0 0 6 6 5 6 g 0 0 0 0 0 4 6 2 10 0 0 0 2 5 3 5 t 0 0 0 0 15 12 7 5 2 1 0 0 10 2 8 6
MA0078.1_rc_shift7 (Sox17_rc)	0.816	0.490	3.080	0.177	0.904	1.499	0.917	4	6	4	4	4	3	3	4.000	4	; oligos_7nt_mkv5_m1 versus MA0078.1_rc (Sox17_rc); m=4/6; ncol2=9; w=9; offset=6; strand=R; shift=7; score= 4; -------sACAATrdr ; cor=0.816; Ncor=0.490; logoDP=3.080; NIcor=0.177; NsEucl=0.904; SSD=1.499; NSW=0.917; rcor=4; rNcor=6; rlogoDP=4; rNIcor=4; rNsEucl=4; rSSD=3; rNSW=3; rank_mean=4.000; match_rank=4 a 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 9 c 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 6 g 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 9 t 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8 7
MA0102.2_rc_shift3 (CEBPA_rc)	0.838	0.503	2.596	0.048	0.893	1.848	0.897	3	5	5	5	6	4	5	4.714	5	; oligos_7nt_mkv5_m1 versus MA0102.2_rc (CEBPA_rc); m=5/6; ncol2=9; w=9; offset=2; strand=R; shift=3; score= 4.7143; ---rTTGcrmaA---- ; cor=0.838; Ncor=0.503; logoDP=2.596; NIcor=0.048; NsEucl=0.893; SSD=1.848; NSW=0.897; rcor=3; rNcor=5; rlogoDP=5; rNIcor=5; rNsEucl=6; rSSD=4; rNSW=5; rank_mean=4.714; match_rank=5 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0 0
MA0019.1_rc_shift0 (Ddit3::Cebpa_rc)	0.756	0.520	0.428	-0.161	0.896	2.597	0.882	6	4	6	6	5	6	6	5.571	6	; oligos_7nt_mkv5_m1 versus MA0019.1_rc (Ddit3::Cebpa_rc); m=6/6; ncol2=12; w=11; offset=-1; strand=R; shift=0; score= 5.5714; ggkATTGCAyyy---- ; cor=0.756; Ncor=0.520; logoDP=0.428; NIcor=-0.161; NsEucl=0.896; SSD=2.597; NSW=0.882; rcor=6; rNcor=4; rlogoDP=6; rNIcor=6; rNsEucl=5; rSSD=6; rNSW=6; rank_mean=5.571; match_rank=6 a 7 3 3 33 0 0 2 1 38 3 7 6 0 0 0 0 c 6 9 5 0 1 0 0 38 0 15 14 12 0 0 0 0 g 26 23 17 6 2 1 33 0 1 3 7 7 0 0 0 0 t 0 4 14 0 36 38 4 0 0 18 11 14 0 0 0 0