One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3.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/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift2 ; 8 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_7nt_m3_shift2 (positions_7nt_m3)																		; positions_7nt_m3; m=0 (reference); ncol1=15; shift=2; ncol=21; --smCCAGGTCATGcyg---- ; Alignment reference a 0 0 44 53 13 15 186 0 3 2 3 192 6 13 41 42 45 0 0 0 0 c 0 0 54 54 154 175 1 0 0 3 191 3 14 18 85 51 33 0 0 0 0 g 0 0 52 43 15 1 4 195 191 5 3 0 16 149 37 31 74 0 0 0 0 t 0 0 48 48 16 7 7 3 4 188 1 3 162 18 35 74 46 0 0 0 0
MA0071.1_shift2 (RORA_1)		0.845	0.564	9.031	0.577	0.913	1.513	0.924	1	1	1	1	2	1	1	1.143	1	; positions_7nt_m3 versus MA0071.1 (RORA_1); m=1/7; ncol2=10; w=10; offset=0; strand=D; shift=2; score= 1.1429; --wwcwAGGTCA--------- ; cor=0.845; Ncor=0.564; logoDP=9.031; NIcor=0.577; NsEucl=0.913; SSD=1.513; NSW=0.924; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.143; match_rank=1 a 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 0 0 c 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 0 0 g 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0
MA0141.1_shift0 (Esrrb)		0.837	0.492	7.951	0.497	0.910	1.621	0.919	2	2	3	2	4	2	2	2.429	2	; positions_7nt_m3 versus MA0141.1 (Esrrb); m=2/7; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 2.4286; rgsyCAAGGTCA--------- ; cor=0.837; Ncor=0.492; logoDP=7.951; NIcor=0.497; NsEucl=0.910; SSD=1.621; NSW=0.919; rcor=2; rNcor=2; rlogoDP=3; rNIcor=2; rNsEucl=4; rSSD=2; rNSW=2; rank_mean=2.429; match_rank=2 a 1054 673 420 259 310 3326 3567 32 21 182 9 3458 0 0 0 0 0 0 0 0 0 c 800 829 1211 1250 2664 32 2 5 12 46 3376 20 0 0 0 0 0 0 0 0 0 g 985 1370 1209 448 627 248 60 3586 3602 244 170 129 0 0 0 0 0 0 0 0 0 t 793 767 805 1693 52 50 27 31 17 3175 85 27 0 0 0 0 0 0 0 0 0
MA0141.2_shift0 (Esrrb)		0.836	0.492	8.042	0.496	0.910	1.635	0.918	3	3	2	3	5	3	4	3.286	3	; positions_7nt_m3 versus MA0141.2 (Esrrb); m=3/7; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 3.2857; rgsyCAAGGTCA--------- ; cor=0.836; Ncor=0.492; logoDP=8.042; NIcor=0.496; NsEucl=0.910; SSD=1.635; NSW=0.918; rcor=3; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=5; rSSD=3; rNSW=4; rank_mean=3.286; match_rank=3 a 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 0 0 0 0 0 0 c 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 0 0 0 0 0 0 g 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 0 0 0 0 0 0 t 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0 0 0 0 0 0 0
MA0258.2_shift6 (ESR2)		0.805	0.466	6.496	0.469	0.914	1.789	0.919	4	4	5	4	1	5	3	3.714	4	; positions_7nt_m3 versus MA0258.2 (ESR2); m=4/7; ncol2=15; w=11; offset=4; strand=D; shift=6; score= 3.7143; ------rGGTCAsmstGaCCy ; cor=0.805; Ncor=0.466; logoDP=6.496; NIcor=0.469; NsEucl=0.914; SSD=1.789; NSW=0.919; rcor=4; rNcor=4; rlogoDP=5; rNIcor=4; rNsEucl=1; rSSD=5; rNSW=3; rank_mean=3.714; match_rank=4 a 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 1111 834 c 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 5854 2708 g 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 0 606 t 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977 1278 4095
MA0159.1_shift6 (RXR::RAR_DR5)		0.793	0.416	5.868	0.419	0.913	1.832	0.917	5	5	6	6	3	6	5	5.143	5	; positions_7nt_m3 versus MA0159.1 (RXR::RAR_DR5); m=5/7; ncol2=17; w=11; offset=4; strand=D; shift=6; score= 5.1429; ------rGkTCAysgrsAGKT ; cor=0.793; Ncor=0.416; logoDP=5.868; NIcor=0.419; NsEucl=0.913; SSD=1.832; NSW=0.917; rcor=5; rNcor=5; rlogoDP=6; rNIcor=6; rNsEucl=3; rSSD=6; rNSW=5; rank_mean=5.143; match_rank=5 a 0 0 0 0 0 0 12 0 1 0 0 22 4 5 5 13 5 17 1 0 2 c 0 0 0 0 0 0 0 0 0 0 18 0 7 8 4 1 6 3 1 1 1 g 0 0 0 0 0 0 11 23 13 1 3 1 5 9 11 7 12 3 20 16 3 t 0 0 0 0 0 0 0 0 9 22 2 0 7 1 3 2 0 0 1 6 17
MA0067.1_shift7 (Pax2)		0.776	0.414	3.256	0.415	0.885	1.695	0.894	6	6	7	7	6	4	6	6.000	6	; positions_7nt_m3 versus MA0067.1 (Pax2); m=6/7; ncol2=8; w=8; offset=5; strand=D; shift=7; score= 6; -------wgTCAykb------ ; cor=0.776; Ncor=0.414; logoDP=3.256; NIcor=0.415; NsEucl=0.885; SSD=1.695; NSW=0.894; rcor=6; rNcor=6; rlogoDP=7; rNIcor=7; rNsEucl=6; rSSD=4; rNSW=6; rank_mean=6.000; match_rank=6 a 0 0 0 0 0 0 0 10 7 3 0 26 2 2 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 7 1 2 28 1 17 0 11 0 0 0 0 0 0 g 0 0 0 0 0 0 0 5 21 0 1 3 1 19 11 0 0 0 0 0 0 t 0 0 0 0 0 0 0 9 2 26 2 1 11 10 8 0 0 0 0 0 0
MA0160.1_shift5 (NR4A2)		0.759	0.405	6.620	0.425	0.869	2.186	0.863	7	7	4	5	7	7	7	6.286	7	; positions_7nt_m3 versus MA0160.1 (NR4A2); m=7/7; ncol2=8; w=8; offset=3; strand=D; shift=5; score= 6.2857; -----aAGGTCAc-------- ; cor=0.759; Ncor=0.405; logoDP=6.620; NIcor=0.425; NsEucl=0.869; SSD=2.186; NSW=0.863; rcor=7; rNcor=7; rlogoDP=4; rNIcor=5; rNsEucl=7; rSSD=7; rNSW=7; rank_mean=6.286; match_rank=7 a 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 0 0 c 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 0 0 0 0 0 0 g 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0 0 0 0 0 0