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/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.2014-09-03.182940_2014-09-03.182940_LkVj4M/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 357 259 768 43 865 5 8 36 26 3 721 847 870 59 359 c 127 176 19 23 8 5 2 2 40 1 79 31 2 182 239 g 172 215 31 695 16 3 17 850 7 885 6 5 14 114 107 t 237 243 75 132 4 880 866 5 820 4 87 10 7 538 188

MA0466.1_rc_shift4 (CEBPB_rc) 0.845 0.620 2.705 0.034 0.915 1.747 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=0.845; Ncor=0.620; logoDP=2.705; NIcor=0.034; NsEucl=0.915; SSD=1.747; 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) 0.845 0.619 4.056 0.122 0.913 1.840 0.916 2 3 2 3 2 3 2 2.429 2
; positions_6nt_m1 versus MA0102.3_rc (CEBPA_rc); m=2/5; ncol2=11; w=11; offset=3; strand=R; shift=3; score= 2.4286; ---krTTrTGCAAt- ; cor=0.845; Ncor=0.619; logoDP=4.056; NIcor=0.122; NsEucl=0.913; SSD=1.840; NSW=0.916; rcor=2; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=2.429; 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) 0.835 0.501 3.041 0.152 0.894 1.828 0.898 3 4 3 2 4 2 4 3.143 3
; positions_6nt_m1 versus MA0102.2_rc (CEBPA_rc); m=3/5; ncol2=9; w=9; offset=4; strand=R; shift=4; score= 3.1429; ----rTTGcrmaA-- ; cor=0.835; Ncor=0.501; logoDP=3.041; NIcor=0.152; NsEucl=0.894; SSD=1.828; NSW=0.898; rcor=3; rNcor=4; rlogoDP=3; rNIcor=2; rNsEucl=4; rSSD=2; rNSW=4; rank_mean=3.143; 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) 0.760 0.456 7.372 0.461 0.884 2.179 0.879 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=0.760; Ncor=0.456; logoDP=7.372; NIcor=0.461; NsEucl=0.884; SSD=2.179; NSW=0.879; 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) 0.807 0.646 0.416 -0.221 0.908 2.428 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=0.807; Ncor=0.646; logoDP=0.416; NIcor=-0.221; NsEucl=0.908; SSD=2.428; 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 357 259 768 43 865 5 8 36 26 3 721 847 870 59 359 c 127 176 19 23 8 5 2 2 40 1 79 31 2 182 239 g 172 215 31 695 16 3 17 850 7 885 6 5 14 114 107 t 237 243 75 132 4 880 866 5 820 4 87 10 7 538 188
MA0466.1_rc_shift4 (CEBPB_rc)	0.845	0.620	2.705	0.034	0.915	1.747	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=0.845; Ncor=0.620; logoDP=2.705; NIcor=0.034; NsEucl=0.915; SSD=1.747; 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)	0.845	0.619	4.056	0.122	0.913	1.840	0.916	2	3	2	3	2	3	2	2.429	2	; positions_6nt_m1 versus MA0102.3_rc (CEBPA_rc); m=2/5; ncol2=11; w=11; offset=3; strand=R; shift=3; score= 2.4286; ---krTTrTGCAAt- ; cor=0.845; Ncor=0.619; logoDP=4.056; NIcor=0.122; NsEucl=0.913; SSD=1.840; NSW=0.916; rcor=2; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=2.429; 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)	0.835	0.501	3.041	0.152	0.894	1.828	0.898	3	4	3	2	4	2	4	3.143	3	; positions_6nt_m1 versus MA0102.2_rc (CEBPA_rc); m=3/5; ncol2=9; w=9; offset=4; strand=R; shift=4; score= 3.1429; ----rTTGcrmaA-- ; cor=0.835; Ncor=0.501; logoDP=3.041; NIcor=0.152; NsEucl=0.894; SSD=1.828; NSW=0.898; rcor=3; rNcor=4; rlogoDP=3; rNIcor=2; rNsEucl=4; rSSD=2; rNSW=4; rank_mean=3.143; 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)	0.760	0.456	7.372	0.461	0.884	2.179	0.879	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=0.760; Ncor=0.456; logoDP=7.372; NIcor=0.461; NsEucl=0.884; SSD=2.179; NSW=0.879; 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)	0.807	0.646	0.416	-0.221	0.908	2.428	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=0.807; Ncor=0.646; logoDP=0.416; NIcor=-0.221; NsEucl=0.908; SSD=2.428; 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