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_8nt_m2/peak-motifs_positions_8nt_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.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m2/peak-motifs_positions_8nt_m2_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: positions_8nt_m2_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
positions_8nt_m2_shift1 (positions_8nt_m2)
; positions_8nt_m2; m=0 (reference); ncol1=16; shift=1; ncol=17; -wrTGATTGTGCAAgad ; Alignment reference a 0 183 173 43 19 589 4 1 23 18 1 24 634 632 19 271 166 c 0 144 131 13 20 12 4 1 4 12 1 586 4 0 72 129 147 g 0 140 178 24 576 24 1 10 594 7 632 3 0 4 406 107 165 t 0 171 156 558 23 13 629 626 17 601 4 25 0 2 141 131 160

MA0466.1_rc_shift5 (CEBPB_rc) 0.871 0.599 2.668 -0.037 0.920 1.536 0.930 1 1 4 5 1 1 1 2.000 1
; positions_8nt_m2 versus MA0466.1_rc (CEBPB_rc); m=1/6; ncol2=11; w=11; offset=4; strand=R; shift=5; score= 2; -----rTkrTGCAATm- ; cor=0.871; Ncor=0.599; logoDP=2.668; NIcor=-0.037; NsEucl=0.920; SSD=1.536; NSW=0.930; rcor=1; rNcor=1; rlogoDP=4; rNIcor=5; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.000; match_rank=1 a 0 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 c 0 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 g 0 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 t 0 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0

MA0102.3_rc_shift4 (CEBPA_rc) 0.862 0.593 4.265 0.040 0.914 1.774 0.919 2 2 3 4 2 3 2 2.571 2
; positions_8nt_m2 versus MA0102.3_rc (CEBPA_rc); m=2/6; ncol2=11; w=11; offset=3; strand=R; shift=4; score= 2.5714; ----krTTrTGCAAt-- ; cor=0.862; Ncor=0.593; logoDP=4.265; NIcor=0.040; NsEucl=0.914; SSD=1.774; NSW=0.919; rcor=2; rNcor=2; rlogoDP=3; rNIcor=4; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=2.571; match_rank=2 a 0 0 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 c 0 0 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 g 0 0 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 t 0 0 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0

MA0102.1_shift6 (Cebpa) 0.780 0.505 6.062 0.491 0.904 2.253 0.898 4 3 2 1 3 5 4 3.143 3
; positions_8nt_m2 versus MA0102.1 (Cebpa); m=3/6; ncol2=12; w=11; offset=5; strand=D; shift=6; score= 3.1429; ------TtkygCAAyvy ; cor=0.780; Ncor=0.505; logoDP=6.062; NIcor=0.491; NsEucl=0.904; SSD=2.253; NSW=0.898; rcor=4; rNcor=3; rlogoDP=2; rNIcor=1; rNsEucl=3; rSSD=5; rNSW=4; rank_mean=3.143; match_rank=3 a 0 0 0 0 0 0 3 1 4 2 4 2 18 18 0 5 2 c 0 0 0 0 0 0 0 1 1 9 2 15 0 0 6 6 5 g 0 0 0 0 0 0 0 4 6 2 10 0 0 0 2 5 3 t 0 0 0 0 0 0 15 12 7 5 2 1 0 0 10 2 8

MA0102.2_rc_shift5 (CEBPA_rc) 0.812 0.457 2.608 0.048 0.885 2.126 0.882 3 4 5 3 5 4 5 4.143 4
; positions_8nt_m2 versus MA0102.2_rc (CEBPA_rc); m=4/6; ncol2=9; w=9; offset=4; strand=R; shift=5; score= 4.1429; -----rTTGcrmaA--- ; cor=0.812; Ncor=0.457; logoDP=2.608; NIcor=0.048; NsEucl=0.885; SSD=2.126; NSW=0.882; rcor=3; rNcor=4; rlogoDP=5; rNIcor=3; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=4.143; match_rank=4 a 0 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0

MA0078.1_shift2 (Sox17) 0.752 0.423 7.158 0.424 0.881 2.296 0.872 6 5 1 2 6 6 6 4.571 5
; positions_8nt_m2 versus MA0078.1 (Sox17); m=5/6; ncol2=9; w=9; offset=1; strand=D; shift=2; score= 4.5714; --yhyATTGTs------ ; cor=0.752; Ncor=0.423; logoDP=7.158; NIcor=0.424; NsEucl=0.881; SSD=2.296; NSW=0.872; rcor=6; rNcor=5; rlogoDP=1; rNIcor=2; rNsEucl=6; rSSD=6; rNSW=6; rank_mean=4.571; match_rank=5 a 0 0 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 c 0 0 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 g 0 0 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 t 0 0 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0

MA0038.1_rc_shift0 (Gfi1_rc) 0.779 0.413 0.367 -0.139 0.895 1.770 0.902 5 6 6 6 4 2 3 4.571 6
; positions_8nt_m2 versus MA0038.1_rc (Gfi1_rc); m=6/6; ncol2=10; w=9; offset=-1; strand=R; shift=0; score= 4.5714; cwgtGATTkr------- ; cor=0.779; Ncor=0.413; logoDP=0.367; NIcor=-0.139; NsEucl=0.895; SSD=1.770; NSW=0.902; rcor=5; rNcor=6; rlogoDP=6; rNIcor=6; rNsEucl=4; rSSD=2; rNSW=3; rank_mean=4.571; match_rank=6 a 5 21 6 13 0 51 0 0 2 15 0 0 0 0 0 0 0 c 28 2 11 2 0 1 0 0 7 9 0 0 0 0 0 0 0 g 13 11 28 7 52 0 0 0 16 20 0 0 0 0 0 0 0 t 7 19 8 31 1 1 53 53 28 9 0 0 0 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
positions_8nt_m2_shift1 (positions_8nt_m2)																	; positions_8nt_m2; m=0 (reference); ncol1=16; shift=1; ncol=17; -wrTGATTGTGCAAgad ; Alignment reference a 0 183 173 43 19 589 4 1 23 18 1 24 634 632 19 271 166 c 0 144 131 13 20 12 4 1 4 12 1 586 4 0 72 129 147 g 0 140 178 24 576 24 1 10 594 7 632 3 0 4 406 107 165 t 0 171 156 558 23 13 629 626 17 601 4 25 0 2 141 131 160
MA0466.1_rc_shift5 (CEBPB_rc)	0.871	0.599	2.668	-0.037	0.920	1.536	0.930	1	1	4	5	1	1	1	2.000	1	; positions_8nt_m2 versus MA0466.1_rc (CEBPB_rc); m=1/6; ncol2=11; w=11; offset=4; strand=R; shift=5; score= 2; -----rTkrTGCAATm- ; cor=0.871; Ncor=0.599; logoDP=2.668; NIcor=-0.037; NsEucl=0.920; SSD=1.536; NSW=0.930; rcor=1; rNcor=1; rlogoDP=4; rNIcor=5; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.000; match_rank=1 a 0 0 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 c 0 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 g 0 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 t 0 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0
MA0102.3_rc_shift4 (CEBPA_rc)	0.862	0.593	4.265	0.040	0.914	1.774	0.919	2	2	3	4	2	3	2	2.571	2	; positions_8nt_m2 versus MA0102.3_rc (CEBPA_rc); m=2/6; ncol2=11; w=11; offset=3; strand=R; shift=4; score= 2.5714; ----krTTrTGCAAt-- ; cor=0.862; Ncor=0.593; logoDP=4.265; NIcor=0.040; NsEucl=0.914; SSD=1.774; NSW=0.919; rcor=2; rNcor=2; rlogoDP=3; rNIcor=4; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=2.571; match_rank=2 a 0 0 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 c 0 0 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 g 0 0 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 t 0 0 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0
MA0102.1_shift6 (Cebpa)	0.780	0.505	6.062	0.491	0.904	2.253	0.898	4	3	2	1	3	5	4	3.143	3	; positions_8nt_m2 versus MA0102.1 (Cebpa); m=3/6; ncol2=12; w=11; offset=5; strand=D; shift=6; score= 3.1429; ------TtkygCAAyvy ; cor=0.780; Ncor=0.505; logoDP=6.062; NIcor=0.491; NsEucl=0.904; SSD=2.253; NSW=0.898; rcor=4; rNcor=3; rlogoDP=2; rNIcor=1; rNsEucl=3; rSSD=5; rNSW=4; rank_mean=3.143; match_rank=3 a 0 0 0 0 0 0 3 1 4 2 4 2 18 18 0 5 2 c 0 0 0 0 0 0 0 1 1 9 2 15 0 0 6 6 5 g 0 0 0 0 0 0 0 4 6 2 10 0 0 0 2 5 3 t 0 0 0 0 0 0 15 12 7 5 2 1 0 0 10 2 8
MA0102.2_rc_shift5 (CEBPA_rc)	0.812	0.457	2.608	0.048	0.885	2.126	0.882	3	4	5	3	5	4	5	4.143	4	; positions_8nt_m2 versus MA0102.2_rc (CEBPA_rc); m=4/6; ncol2=9; w=9; offset=4; strand=R; shift=5; score= 4.1429; -----rTTGcrmaA--- ; cor=0.812; Ncor=0.457; logoDP=2.608; NIcor=0.048; NsEucl=0.885; SSD=2.126; NSW=0.882; rcor=3; rNcor=4; rlogoDP=5; rNIcor=3; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=4.143; match_rank=4 a 0 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0078.1_shift2 (Sox17)	0.752	0.423	7.158	0.424	0.881	2.296	0.872	6	5	1	2	6	6	6	4.571	5	; positions_8nt_m2 versus MA0078.1 (Sox17); m=5/6; ncol2=9; w=9; offset=1; strand=D; shift=2; score= 4.5714; --yhyATTGTs------ ; cor=0.752; Ncor=0.423; logoDP=7.158; NIcor=0.424; NsEucl=0.881; SSD=2.296; NSW=0.872; rcor=6; rNcor=5; rlogoDP=1; rNIcor=2; rNsEucl=6; rSSD=6; rNSW=6; rank_mean=4.571; match_rank=5 a 0 0 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 c 0 0 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 g 0 0 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 t 0 0 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0
MA0038.1_rc_shift0 (Gfi1_rc)	0.779	0.413	0.367	-0.139	0.895	1.770	0.902	5	6	6	6	4	2	3	4.571	6	; positions_8nt_m2 versus MA0038.1_rc (Gfi1_rc); m=6/6; ncol2=10; w=9; offset=-1; strand=R; shift=0; score= 4.5714; cwgtGATTkr------- ; cor=0.779; Ncor=0.413; logoDP=0.367; NIcor=-0.139; NsEucl=0.895; SSD=1.770; NSW=0.902; rcor=5; rNcor=6; rlogoDP=6; rNIcor=6; rNsEucl=4; rSSD=2; rNSW=3; rank_mean=4.571; match_rank=6 a 5 21 6 13 0 51 0 0 2 15 0 0 0 0 0 0 0 c 28 2 11 2 0 1 0 0 7 9 0 0 0 0 0 0 0 g 13 11 28 7 52 0 0 0 16 20 0 0 0 0 0 0 0 t 7 19 8 31 1 1 53 53 28 9 0 0 0 0 0 0 0