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_7nt_m2/peak-motifs_positions_7nt_m2.tf -format2 tf -file2 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/peak-motifs_custom_motif_db.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_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_Schmidt_CEBPa_motif

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m2_shift0 (positions_7nt_m2)                                
; positions_7nt_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; rmAGATTGCACAACTyt
; Alignment reference
a	94	132	260	16	314	0	0	10	2	311	7	331	333	6	35	67	73
c	71	85	4	10	5	0	0	0	330	11	318	3	0	296	15	105	76
g	95	77	9	277	13	1	2	309	1	1	1	0	0	7	2	77	54
t	74	40	61	31	2	333	332	15	1	11	8	0	1	25	282	85	131
do560+do843_mmus_cebpa_liver_meme_top_m1_shift4 (do560+do843_mmus_cebpa_liver_meme_top_m1) 0.869 0.563 9.570 0.543 0.913 1.819 0.917 1 1 1 1 1 1 1 1.000 1
; positions_7nt_m2 versus do560+do843_mmus_cebpa_liver_meme_top_m1; m=1/1; ncol2=11; w=11; offset=4; strand=D; shift=4; score=      1; ----rTTGCacMAym--
; cor=0.869; Ncor=0.563; logoDP=9.570; NIcor=0.543; NsEucl=0.913; SSD=1.819; NSW=0.917; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a	0	0	0	0	204	0	0	35	0	259	80	300	431	1	143	0	0
c	0	0	0	0	69	0	0	0	431	48	258	130	0	169	145	0	0
g	0	0	0	0	138	0	0	365	0	85	0	0	0	78	60	0	0
t	0	0	0	0	20	431	431	31	0	39	93	1	0	183	83	0	0