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_m3/peak-motifs_positions_6nt_m3.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_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_Schmidt_CEBPa_motif

One-to-n matrix alignment; reference matrix: positions_6nt_m3_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_6nt_m3_shift0 (positions_6nt_m3)                                
; positions_6nt_m3; m=0 (reference); ncol1=13; shift=0; ncol=14; rmAGTTGCAAAay-
; Alignment reference
a	115	113	342	0	0	0	0	0	343	342	344	223	67	0
c	76	100	2	0	0	1	0	344	0	0	0	27	93	0
g	90	71	0	344	0	0	344	0	1	0	0	50	71	0
t	63	60	0	0	344	343	0	0	0	2	0	44	113	0
do560+do843_mmus_cebpa_liver_meme_top_m1_shift3 (do560+do843_mmus_cebpa_liver_meme_top_m1) 0.782 0.558 8.249 0.522 0.890 2.433 0.878 1 1 1 1 1 1 1 1.000 1
; positions_6nt_m3 versus do560+do843_mmus_cebpa_liver_meme_top_m1; m=1/1; ncol2=11; w=10; offset=3; strand=D; shift=3; score=      1; ---rTTGCacMAym
; cor=0.782; Ncor=0.558; logoDP=8.249; NIcor=0.522; NsEucl=0.890; SSD=2.433; NSW=0.878; 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	204	0	0	35	0	259	80	300	431	1	143
c	0	0	0	69	0	0	0	431	48	258	130	0	169	145
g	0	0	0	138	0	0	365	0	85	0	0	0	78	60
t	0	0	0	20	431	431	31	0	39	93	1	0	183	83