One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5.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.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift2 ; 5 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
oligos_7nt_mkv5_m5_shift2 (oligos_7nt_mkv5_m5)                                
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --wrTTGCTCAAya
; Alignment reference
a	0	0	798	1165	0	0	0	0	5	0	2811	2811	291	989
c	0	0	484	563	0	1	0	2811	0	2811	0	0	857	675
g	0	0	602	755	0	0	2811	0	6	0	0	0	492	465
t	0	0	927	328	2811	2810	0	0	2800	0	0	0	1171	682
MA0102.3_shift3 (CEBPA) 0.803 0.736 9.717 0.722 0.904 2.210 0.900 1 1 1 1 1 1 1 1.000 1
; oligos_7nt_mkv5_m5 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=1; strand=D; shift=3; score=      1; ---aTTGCAyAAym
; cor=0.803; Ncor=0.736; logoDP=9.717; NIcor=0.722; NsEucl=0.904; SSD=2.210; NSW=0.900; 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	10351	0	0	705	0	11956	2660	12226	15318	0	5804
c	0	0	0	1332	0	0	0	15318	1274	7654	3092	0	5688	4963
g	0	0	0	3635	0	0	11304	0	1066	0	0	0	1804	890
t	0	0	0	0	15318	15318	3309	0	1022	5004	0	0	7826	3661
MA0466.1_shift2 (CEBPB) 0.779 0.714 9.501 0.691 0.899 2.478 0.887 3 2 2 2 2 4 2 2.429 2
; oligos_7nt_mkv5_m5 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=0; strand=D; shift=2; score= 2.4286; --kATTGCAymAy-
; cor=0.779; Ncor=0.714; logoDP=9.501; NIcor=0.691; NsEucl=0.899; SSD=2.478; NSW=0.887; rcor=3; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=4; rNSW=2; rank_mean=2.429; match_rank=2
a	0	0	13006	75198	0	0	4556	0	74715	8654	60151	99494	0	0
c	0	0	10026	5868	0	0	0	99494	5478	51954	39343	0	36038	0
g	0	0	33617	18428	0	0	75531	0	10015	0	0	0	2043	0
t	0	0	42845	0	99494	99494	19407	0	9286	38886	0	0	61413	0
MA0102.2_rc_shift3 (CEBPA_rc) 0.784 0.588 2.577 0.065 0.880 2.350 0.869 2 3 3 3 4 2 4 3.000 3
; oligos_7nt_mkv5_m5 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=1; strand=R; shift=3; score=      3; ---rTTGcrmaA--
; cor=0.784; Ncor=0.588; logoDP=2.577; NIcor=0.065; NsEucl=0.880; SSD=2.350; NSW=0.869; rcor=2; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=4; rSSD=2; rNSW=4; rank_mean=3.000; match_rank=3
a	0	0	0	10	0	0	1	2	5	7	12	15	0	0
c	0	0	0	2	0	0	0	10	2	6	4	0	0	0
g	0	0	0	6	0	0	15	2	9	1	1	0	0	0
t	0	0	0	0	18	18	2	4	2	4	1	3	0	0
MA0102.1_rc_shift0 (Cebpa_rc) 0.778 0.556 0.504 -0.105 0.890 2.408 0.880 4 4 4 4 3 3 3 3.571 4
; oligos_7nt_mkv5_m5 versus MA0102.1_rc (Cebpa_rc); m=4/4; ncol2=12; w=10; offset=-2; strand=R; shift=0; score= 3.5714; vrbrTTGcrmaA--
; cor=0.778; Ncor=0.556; logoDP=0.504; NIcor=-0.105; NsEucl=0.890; SSD=2.408; NSW=0.880; rcor=4; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.571; match_rank=4
a	6	8	2	10	0	0	1	2	5	7	12	15	0	0
c	5	3	5	2	0	0	0	10	2	6	4	0	0	0
g	6	5	6	6	0	0	15	2	9	1	1	0	0	0
t	1	2	5	0	18	18	2	4	2	4	1	3	0	0