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_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2.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_8nt_mkv6_m2/peak-motifs_oligos_8nt_mkv6_m2_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m2_shift1 ; 6 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_m2_shift1 (oligos_8nt_mkv6_m2)
; oligos_8nt_mkv6_m2; m=0 (reference); ncol1=14; shift=1; ncol=15; -wkATTGTGAAATaw ; Alignment reference a 0 1314 898 3074 24 26 71 73 20 3257 3961 4033 93 1624 1211 c 0 660 557 241 11 10 15 263 2 360 61 7 335 985 878 g 0 993 1040 571 8 33 3952 36 4011 11 6 7 248 674 788 t 0 1090 1562 171 4014 3988 19 3685 24 429 29 10 3381 774 1180

MA0102.3_rc_shift2 (CEBPA_rc) 0.879 0.691 4.259 0.146 0.924 1.396 0.937 1 1 2 3 1 2 1 1.571 1
; oligos_8nt_mkv6_m2 versus MA0102.3_rc (CEBPA_rc); m=1/5; ncol2=11; w=11; offset=1; strand=R; shift=2; score= 1.5714; --krTTrTGCAAt-- ; cor=0.879; Ncor=0.691; logoDP=4.259; NIcor=0.146; NsEucl=0.924; SSD=1.396; NSW=0.937; rcor=1; rNcor=1; rlogoDP=2; rNIcor=3; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.571; match_rank=1 a 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 c 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 g 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 t 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0

MA0078.1_shift0 (Sox17) 0.852 0.454 6.713 0.449 0.905 1.143 0.929 3 5 1 1 4 1 2 2.429 2
; oligos_8nt_mkv6_m2 versus MA0078.1 (Sox17); m=2/5; ncol2=9; w=8; offset=-1; strand=D; shift=0; score= 2.4286; yhyATTGTs------ ; cor=0.852; Ncor=0.454; logoDP=6.713; NIcor=0.449; NsEucl=0.905; SSD=1.143; NSW=0.929; rcor=3; rNcor=5; rlogoDP=1; rNIcor=1; rNsEucl=4; rSSD=1; rNSW=2; rank_mean=2.429; match_rank=2 a 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 c 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 g 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 t 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0

MA0466.1_rc_shift3 (CEBPB_rc) 0.860 0.676 2.835 0.043 0.918 1.608 0.927 2 2 4 4 2 3 3 2.857 3
; oligos_8nt_mkv6_m2 versus MA0466.1_rc (CEBPB_rc); m=3/5; ncol2=11; w=11; offset=2; strand=R; shift=3; score= 2.8571; ---rTkrTGCAATm- ; cor=0.860; Ncor=0.676; logoDP=2.835; NIcor=0.043; NsEucl=0.918; SSD=1.608; NSW=0.927; rcor=2; rNcor=2; rlogoDP=4; rNIcor=4; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.857; match_rank=3 a 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 c 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 g 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 t 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0

MA0102.2_rc_shift3 (CEBPA_rc) 0.850 0.547 3.151 0.175 0.900 1.627 0.910 4 4 3 2 5 4 5 3.857 4
; oligos_8nt_mkv6_m2 versus MA0102.2_rc (CEBPA_rc); m=4/5; ncol2=9; w=9; offset=2; strand=R; shift=3; score= 3.8571; ---rTTGcrmaA--- ; cor=0.850; Ncor=0.547; logoDP=3.151; NIcor=0.175; NsEucl=0.900; SSD=1.627; NSW=0.910; rcor=4; rNcor=4; rlogoDP=3; rNIcor=2; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=3.857; match_rank=4 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0

MA0102.1_rc_shift0 (Cebpa_rc) 0.840 0.616 0.283 -0.189 0.916 1.717 0.922 5 3 5 5 3 5 4 4.286 5
; oligos_8nt_mkv6_m2 versus MA0102.1_rc (Cebpa_rc); m=5/5; ncol2=12; w=11; offset=-1; strand=R; shift=0; score= 4.2857; vrbrTTGcrmaA--- ; cor=0.840; Ncor=0.616; logoDP=0.283; NIcor=-0.189; NsEucl=0.916; SSD=1.717; NSW=0.922; rcor=5; rNcor=3; rlogoDP=5; rNIcor=5; rNsEucl=3; rSSD=5; rNSW=4; rank_mean=4.286; match_rank=5 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 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_m2_shift1 (oligos_8nt_mkv6_m2)																	; oligos_8nt_mkv6_m2; m=0 (reference); ncol1=14; shift=1; ncol=15; -wkATTGTGAAATaw ; Alignment reference a 0 1314 898 3074 24 26 71 73 20 3257 3961 4033 93 1624 1211 c 0 660 557 241 11 10 15 263 2 360 61 7 335 985 878 g 0 993 1040 571 8 33 3952 36 4011 11 6 7 248 674 788 t 0 1090 1562 171 4014 3988 19 3685 24 429 29 10 3381 774 1180
MA0102.3_rc_shift2 (CEBPA_rc)	0.879	0.691	4.259	0.146	0.924	1.396	0.937	1	1	2	3	1	2	1	1.571	1	; oligos_8nt_mkv6_m2 versus MA0102.3_rc (CEBPA_rc); m=1/5; ncol2=11; w=11; offset=1; strand=R; shift=2; score= 1.5714; --krTTrTGCAAt-- ; cor=0.879; Ncor=0.691; logoDP=4.259; NIcor=0.146; NsEucl=0.924; SSD=1.396; NSW=0.937; rcor=1; rNcor=1; rlogoDP=2; rNIcor=3; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.571; match_rank=1 a 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 c 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 g 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 t 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0
MA0078.1_shift0 (Sox17)	0.852	0.454	6.713	0.449	0.905	1.143	0.929	3	5	1	1	4	1	2	2.429	2	; oligos_8nt_mkv6_m2 versus MA0078.1 (Sox17); m=2/5; ncol2=9; w=8; offset=-1; strand=D; shift=0; score= 2.4286; yhyATTGTs------ ; cor=0.852; Ncor=0.454; logoDP=6.713; NIcor=0.449; NsEucl=0.905; SSD=1.143; NSW=0.929; rcor=3; rNcor=5; rlogoDP=1; rNIcor=1; rNsEucl=4; rSSD=1; rNSW=2; rank_mean=2.429; match_rank=2 a 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 c 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 g 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 t 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0
MA0466.1_rc_shift3 (CEBPB_rc)	0.860	0.676	2.835	0.043	0.918	1.608	0.927	2	2	4	4	2	3	3	2.857	3	; oligos_8nt_mkv6_m2 versus MA0466.1_rc (CEBPB_rc); m=3/5; ncol2=11; w=11; offset=2; strand=R; shift=3; score= 2.8571; ---rTkrTGCAATm- ; cor=0.860; Ncor=0.676; logoDP=2.835; NIcor=0.043; NsEucl=0.918; SSD=1.608; NSW=0.927; rcor=2; rNcor=2; rlogoDP=4; rNIcor=4; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.857; match_rank=3 a 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 c 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 g 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 t 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0
MA0102.2_rc_shift3 (CEBPA_rc)	0.850	0.547	3.151	0.175	0.900	1.627	0.910	4	4	3	2	5	4	5	3.857	4	; oligos_8nt_mkv6_m2 versus MA0102.2_rc (CEBPA_rc); m=4/5; ncol2=9; w=9; offset=2; strand=R; shift=3; score= 3.8571; ---rTTGcrmaA--- ; cor=0.850; Ncor=0.547; logoDP=3.151; NIcor=0.175; NsEucl=0.900; SSD=1.627; NSW=0.910; rcor=4; rNcor=4; rlogoDP=3; rNIcor=2; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=3.857; match_rank=4 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.1_rc_shift0 (Cebpa_rc)	0.840	0.616	0.283	-0.189	0.916	1.717	0.922	5	3	5	5	3	5	4	4.286	5	; oligos_8nt_mkv6_m2 versus MA0102.1_rc (Cebpa_rc); m=5/5; ncol2=12; w=11; offset=-1; strand=R; shift=0; score= 4.2857; vrbrTTGcrmaA--- ; cor=0.840; Ncor=0.616; logoDP=0.283; NIcor=-0.189; NsEucl=0.916; SSD=1.717; NSW=0.922; rcor=5; rNcor=3; rlogoDP=5; rNIcor=5; rNsEucl=3; rSSD=5; rNSW=4; rank_mean=4.286; match_rank=5 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0