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/positions_6nt_m1/peak-motifs_positions_6nt_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/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 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
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; wwAGATTGTGAAAtm ; Alignment reference a 358 258 771 43 867 5 8 37 26 3 721 851 886 58 368 c 124 176 20 25 8 5 2 2 40 1 82 31 1 184 243 g 173 214 31 694 17 3 17 852 7 889 6 5 6 111 102 t 242 249 75 135 5 884 870 6 824 4 88 10 4 544 184

MA0466.1_rc_shift4 (CEBPB_rc) 0.848 0.622 2.740 0.033 0.915 1.730 0.921 1 2 4 4 1 1 1 2.000 1
; positions_6nt_m1 versus MA0466.1_rc (CEBPB_rc); m=1/5; ncol2=11; w=11; offset=4; strand=R; shift=4; score= 2; ----rTkrTGCAATm ; cor=0.848; Ncor=0.622; logoDP=2.740; NIcor=0.033; NsEucl=0.915; SSD=1.730; NSW=0.921; rcor=1; rNcor=2; rlogoDP=4; rNIcor=4; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.000; match_rank=1 a 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006

MA0102.3_rc_shift3 (CEBPA_rc) 0.847 0.621 4.050 0.121 0.913 1.820 0.917 2 3 2 3 2 2 2 2.286 2
; positions_6nt_m1 versus MA0102.3_rc (CEBPA_rc); m=2/5; ncol2=11; w=11; offset=3; strand=R; shift=3; score= 2.2857; ---krTTrTGCAAt- ; cor=0.847; Ncor=0.621; logoDP=4.050; NIcor=0.121; NsEucl=0.913; SSD=1.820; NSW=0.917; rcor=2; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.286; match_rank=2 a 0 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 c 0 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 g 0 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 t 0 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0

MA0102.2_rc_shift4 (CEBPA_rc) 0.836 0.502 3.028 0.151 0.894 1.826 0.899 3 4 3 2 4 3 4 3.286 3
; positions_6nt_m1 versus MA0102.2_rc (CEBPA_rc); m=3/5; ncol2=9; w=9; offset=4; strand=R; shift=4; score= 3.2857; ----rTTGcrmaA-- ; cor=0.836; Ncor=0.502; logoDP=3.028; NIcor=0.151; NsEucl=0.894; SSD=1.826; NSW=0.899; rcor=3; rNcor=4; rlogoDP=3; rNIcor=2; rNsEucl=4; rSSD=3; rNSW=4; rank_mean=3.286; match_rank=3 a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0

MA0078.1_shift1 (Sox17) 0.761 0.456 7.347 0.462 0.884 2.168 0.880 5 5 1 1 5 4 5 3.714 4
; positions_6nt_m1 versus MA0078.1 (Sox17); m=4/5; ncol2=9; w=9; offset=1; strand=D; shift=1; score= 3.7143; -yhyATTGTs----- ; cor=0.761; Ncor=0.456; logoDP=7.347; NIcor=0.462; NsEucl=0.884; SSD=2.168; NSW=0.880; rcor=5; rNcor=5; rlogoDP=1; rNIcor=1; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=3.714; match_rank=4 a 0 7 8 3 30 0 0 0 0 0 0 0 0 0 0 c 0 9 8 18 0 1 0 0 0 17 0 0 0 0 0 g 0 6 4 1 0 0 0 31 2 10 0 0 0 0 0 t 0 9 11 9 1 30 31 0 29 4 0 0 0 0 0

MA0102.1_rc_shift1 (Cebpa_rc) 0.808 0.646 0.416 -0.221 0.908 2.422 0.899 4 1 5 5 3 5 3 3.714 5
; positions_6nt_m1 versus MA0102.1_rc (Cebpa_rc); m=5/5; ncol2=12; w=12; offset=1; strand=R; shift=1; score= 3.7143; -vrbrTTGcrmaA-- ; cor=0.808; Ncor=0.646; logoDP=0.416; NIcor=-0.221; NsEucl=0.908; SSD=2.422; NSW=0.899; rcor=4; rNcor=1; rlogoDP=5; rNIcor=5; rNsEucl=3; rSSD=5; rNSW=3; rank_mean=3.714; match_rank=5 a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)																	; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; wwAGATTGTGAAAtm ; Alignment reference a 358 258 771 43 867 5 8 37 26 3 721 851 886 58 368 c 124 176 20 25 8 5 2 2 40 1 82 31 1 184 243 g 173 214 31 694 17 3 17 852 7 889 6 5 6 111 102 t 242 249 75 135 5 884 870 6 824 4 88 10 4 544 184
MA0466.1_rc_shift4 (CEBPB_rc)	0.848	0.622	2.740	0.033	0.915	1.730	0.921	1	2	4	4	1	1	1	2.000	1	; positions_6nt_m1 versus MA0466.1_rc (CEBPB_rc); m=1/5; ncol2=11; w=11; offset=4; strand=R; shift=4; score= 2; ----rTkrTGCAATm ; cor=0.848; Ncor=0.622; logoDP=2.740; NIcor=0.033; NsEucl=0.915; SSD=1.730; NSW=0.921; rcor=1; rNcor=2; rlogoDP=4; rNIcor=4; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.000; match_rank=1 a 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006
MA0102.3_rc_shift3 (CEBPA_rc)	0.847	0.621	4.050	0.121	0.913	1.820	0.917	2	3	2	3	2	2	2	2.286	2	; positions_6nt_m1 versus MA0102.3_rc (CEBPA_rc); m=2/5; ncol2=11; w=11; offset=3; strand=R; shift=3; score= 2.2857; ---krTTrTGCAAt- ; cor=0.847; Ncor=0.621; logoDP=4.050; NIcor=0.121; NsEucl=0.913; SSD=1.820; NSW=0.917; rcor=2; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.286; match_rank=2 a 0 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 c 0 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 g 0 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 t 0 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0
MA0102.2_rc_shift4 (CEBPA_rc)	0.836	0.502	3.028	0.151	0.894	1.826	0.899	3	4	3	2	4	3	4	3.286	3	; positions_6nt_m1 versus MA0102.2_rc (CEBPA_rc); m=3/5; ncol2=9; w=9; offset=4; strand=R; shift=4; score= 3.2857; ----rTTGcrmaA-- ; cor=0.836; Ncor=0.502; logoDP=3.028; NIcor=0.151; NsEucl=0.894; SSD=1.826; NSW=0.899; rcor=3; rNcor=4; rlogoDP=3; rNIcor=2; rNsEucl=4; rSSD=3; rNSW=4; rank_mean=3.286; match_rank=3 a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0
MA0078.1_shift1 (Sox17)	0.761	0.456	7.347	0.462	0.884	2.168	0.880	5	5	1	1	5	4	5	3.714	4	; positions_6nt_m1 versus MA0078.1 (Sox17); m=4/5; ncol2=9; w=9; offset=1; strand=D; shift=1; score= 3.7143; -yhyATTGTs----- ; cor=0.761; Ncor=0.456; logoDP=7.347; NIcor=0.462; NsEucl=0.884; SSD=2.168; NSW=0.880; rcor=5; rNcor=5; rlogoDP=1; rNIcor=1; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=3.714; match_rank=4 a 0 7 8 3 30 0 0 0 0 0 0 0 0 0 0 c 0 9 8 18 0 1 0 0 0 17 0 0 0 0 0 g 0 6 4 1 0 0 0 31 2 10 0 0 0 0 0 t 0 9 11 9 1 30 31 0 29 4 0 0 0 0 0
MA0102.1_rc_shift1 (Cebpa_rc)	0.808	0.646	0.416	-0.221	0.908	2.422	0.899	4	1	5	5	3	5	3	3.714	5	; positions_6nt_m1 versus MA0102.1_rc (Cebpa_rc); m=5/5; ncol2=12; w=12; offset=1; strand=R; shift=1; score= 3.7143; -vrbrTTGcrmaA-- ; cor=0.808; Ncor=0.646; logoDP=0.416; NIcor=-0.221; NsEucl=0.908; SSD=2.422; NSW=0.899; rcor=4; rNcor=1; rlogoDP=5; rNIcor=5; rNsEucl=3; rSSD=5; rNSW=3; rank_mean=3.714; match_rank=5 a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0