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_m1/peak-motifs_oligos_8nt_mkv6_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.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_8nt_mkv6_m1/peak-motifs_oligos_8nt_mkv6_m1_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m1_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
oligos_8nt_mkv6_m1_shift0 (oligos_8nt_mkv6_m1)
; oligos_8nt_mkv6_m1; m=0 (reference); ncol1=15; shift=0; ncol=16; atGGTTGCACAATah- ; Alignment reference a 916 519 193 371 2 4 54 1 2146 57 2247 2242 18 885 631 0 c 427 233 24 77 4 0 3 2252 32 2134 18 4 475 510 578 0 g 477 406 1804 1760 2 8 2128 5 32 14 0 14 49 354 370 0 t 447 1109 246 59 2259 2255 82 9 57 62 2 7 1725 518 688 0

MA0102.3_shift3 (CEBPA) 0.905 0.664 9.835 0.645 0.931 1.166 0.947 1 1 1 1 1 2 1 1.143 1
; oligos_8nt_mkv6_m1 versus MA0102.3 (CEBPA); m=1/6; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 1.1429; ---aTTGCAyAAym-- ; cor=0.905; Ncor=0.664; logoDP=9.835; NIcor=0.645; NsEucl=0.931; SSD=1.166; NSW=0.947; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.143; match_rank=1 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

MA0466.1_shift2 (CEBPB) 0.857 0.629 9.666 0.600 0.914 1.791 0.919 2 2 2 2 2 3 3 2.286 2
; oligos_8nt_mkv6_m1 versus MA0466.1 (CEBPB); m=2/6; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 2.2857; --kATTGCAymAy--- ; cor=0.857; Ncor=0.629; logoDP=9.666; NIcor=0.600; NsEucl=0.914; SSD=1.791; NSW=0.919; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.286; match_rank=2 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

MA0078.1_rc_shift7 (Sox17_rc) 0.854 0.427 2.638 0.134 0.906 1.140 0.929 3 6 5 5 3 1 2 3.571 3
; oligos_8nt_mkv6_m1 versus MA0078.1_rc (Sox17_rc); m=3/6; ncol2=9; w=8; offset=7; strand=R; shift=7; score= 3.5714; -------sACAATrdr ; cor=0.854; Ncor=0.427; logoDP=2.638; NIcor=0.134; NsEucl=0.906; SSD=1.140; NSW=0.929; rcor=3; rNcor=6; rlogoDP=5; rNIcor=5; rNsEucl=3; rSSD=1; rNSW=2; rank_mean=3.571; match_rank=3 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_shift4 (CEBPA) 0.819 0.492 6.238 0.466 0.889 2.012 0.888 4 5 3 4 6 4 5 4.429 4
; oligos_8nt_mkv6_m1 versus MA0102.2 (CEBPA); m=4/6; ncol2=9; w=9; offset=4; strand=D; shift=4; score= 4.4286; ----TtkygCAAy--- ; cor=0.819; Ncor=0.492; logoDP=6.238; NIcor=0.466; NsEucl=0.889; SSD=2.012; NSW=0.888; rcor=4; rNcor=5; rlogoDP=3; rNIcor=4; rNsEucl=6; rSSD=4; rNSW=5; rank_mean=4.429; match_rank=4 a 0 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0

MA0102.1_rc_shift0 (Cebpa_rc) 0.771 0.617 0.293 -0.165 0.904 2.655 0.889 5 3 6 6 4 5 4 4.714 5
; oligos_8nt_mkv6_m1 versus MA0102.1_rc (Cebpa_rc); m=5/6; ncol2=12; w=12; offset=0; strand=R; shift=0; score= 4.7143; vrbrTTGcrmaA---- ; cor=0.771; Ncor=0.617; logoDP=0.293; NIcor=-0.165; NsEucl=0.904; SSD=2.655; NSW=0.889; rcor=5; rNcor=3; rlogoDP=6; rNIcor=6; rNsEucl=4; rSSD=5; rNSW=4; rank_mean=4.714; match_rank=5 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0 0

MA0043.1_shift2 (HLF) 0.753 0.602 6.217 0.584 0.899 2.942 0.877 6 4 4 3 5 6 6 4.857 6
; oligos_8nt_mkv6_m1 versus MA0043.1 (HLF); m=6/6; ncol2=12; w=12; offset=2; strand=D; shift=2; score= 4.8571; --krTTACryAAth-- ; cor=0.753; Ncor=0.602; logoDP=6.217; NIcor=0.584; NsEucl=0.899; SSD=2.942; NSW=0.877; rcor=6; rNcor=4; rlogoDP=4; rNIcor=3; rNsEucl=5; rSSD=6; rNSW=6; rank_mean=4.857; match_rank=6 a 0 0 1 6 1 0 13 0 6 0 13 15 2 5 0 0 c 0 0 4 0 0 0 1 15 0 9 4 0 3 5 0 0 g 0 0 8 12 0 3 2 1 12 0 1 1 1 3 0 0 t 0 0 5 0 17 15 2 2 0 9 0 2 12 5 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_m1_shift0 (oligos_8nt_mkv6_m1)																	; oligos_8nt_mkv6_m1; m=0 (reference); ncol1=15; shift=0; ncol=16; atGGTTGCACAATah- ; Alignment reference a 916 519 193 371 2 4 54 1 2146 57 2247 2242 18 885 631 0 c 427 233 24 77 4 0 3 2252 32 2134 18 4 475 510 578 0 g 477 406 1804 1760 2 8 2128 5 32 14 0 14 49 354 370 0 t 447 1109 246 59 2259 2255 82 9 57 62 2 7 1725 518 688 0
MA0102.3_shift3 (CEBPA)	0.905	0.664	9.835	0.645	0.931	1.166	0.947	1	1	1	1	1	2	1	1.143	1	; oligos_8nt_mkv6_m1 versus MA0102.3 (CEBPA); m=1/6; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 1.1429; ---aTTGCAyAAym-- ; cor=0.905; Ncor=0.664; logoDP=9.835; NIcor=0.645; NsEucl=0.931; SSD=1.166; NSW=0.947; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.143; match_rank=1 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
MA0466.1_shift2 (CEBPB)	0.857	0.629	9.666	0.600	0.914	1.791	0.919	2	2	2	2	2	3	3	2.286	2	; oligos_8nt_mkv6_m1 versus MA0466.1 (CEBPB); m=2/6; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 2.2857; --kATTGCAymAy--- ; cor=0.857; Ncor=0.629; logoDP=9.666; NIcor=0.600; NsEucl=0.914; SSD=1.791; NSW=0.919; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.286; match_rank=2 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
MA0078.1_rc_shift7 (Sox17_rc)	0.854	0.427	2.638	0.134	0.906	1.140	0.929	3	6	5	5	3	1	2	3.571	3	; oligos_8nt_mkv6_m1 versus MA0078.1_rc (Sox17_rc); m=3/6; ncol2=9; w=8; offset=7; strand=R; shift=7; score= 3.5714; -------sACAATrdr ; cor=0.854; Ncor=0.427; logoDP=2.638; NIcor=0.134; NsEucl=0.906; SSD=1.140; NSW=0.929; rcor=3; rNcor=6; rlogoDP=5; rNIcor=5; rNsEucl=3; rSSD=1; rNSW=2; rank_mean=3.571; match_rank=3 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_shift4 (CEBPA)	0.819	0.492	6.238	0.466	0.889	2.012	0.888	4	5	3	4	6	4	5	4.429	4	; oligos_8nt_mkv6_m1 versus MA0102.2 (CEBPA); m=4/6; ncol2=9; w=9; offset=4; strand=D; shift=4; score= 4.4286; ----TtkygCAAy--- ; cor=0.819; Ncor=0.492; logoDP=6.238; NIcor=0.466; NsEucl=0.889; SSD=2.012; NSW=0.888; rcor=4; rNcor=5; rlogoDP=3; rNIcor=4; rNsEucl=6; rSSD=4; rNSW=5; rank_mean=4.429; match_rank=4 a 0 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 c 0 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 g 0 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 t 0 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
MA0102.1_rc_shift0 (Cebpa_rc)	0.771	0.617	0.293	-0.165	0.904	2.655	0.889	5	3	6	6	4	5	4	4.714	5	; oligos_8nt_mkv6_m1 versus MA0102.1_rc (Cebpa_rc); m=5/6; ncol2=12; w=12; offset=0; strand=R; shift=0; score= 4.7143; vrbrTTGcrmaA---- ; cor=0.771; Ncor=0.617; logoDP=0.293; NIcor=-0.165; NsEucl=0.904; SSD=2.655; NSW=0.889; rcor=5; rNcor=3; rlogoDP=6; rNIcor=6; rNsEucl=4; rSSD=5; rNSW=4; rank_mean=4.714; match_rank=5 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0 0
MA0043.1_shift2 (HLF)	0.753	0.602	6.217	0.584	0.899	2.942	0.877	6	4	4	3	5	6	6	4.857	6	; oligos_8nt_mkv6_m1 versus MA0043.1 (HLF); m=6/6; ncol2=12; w=12; offset=2; strand=D; shift=2; score= 4.8571; --krTTACryAAth-- ; cor=0.753; Ncor=0.602; logoDP=6.217; NIcor=0.584; NsEucl=0.899; SSD=2.942; NSW=0.877; rcor=6; rNcor=4; rlogoDP=4; rNIcor=3; rNsEucl=5; rSSD=6; rNSW=6; rank_mean=4.857; match_rank=6 a 0 0 1 6 1 0 13 0 6 0 13 15 2 5 0 0 c 0 0 4 0 0 0 1 15 0 9 4 0 3 5 0 0 g 0 0 8 12 0 3 2 1 12 0 1 1 1 3 0 0 t 0 0 5 0 17 15 2 2 0 9 0 2 12 5 0 0