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/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4.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/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift0 ; 4 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_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)                                
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=13; shift=0; ncol=14; ttTTCTTTTCTtt-
; Alignment reference
a	284	285	145	199	3	0	6	8	4	1	7	298	281	0
c	250	209	51	47	1336	0	0	0	1	1338	14	258	292	0
g	215	182	43	30	0	11	1	0	0	0	46	236	177	0
t	590	663	1100	1063	0	1328	1332	1331	1334	0	1272	547	589	0
MA0035.3_shift2 (Gata1) 0.767 0.649 9.313 0.658 0.896 2.612 0.881 2 1 1 1 1 3 1 1.429 1
; oligos_6nt_mkv4_m4 versus MA0035.3 (Gata1); m=1/3; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 1.4286; --tyCTTATCTsy-
; cor=0.767; Ncor=0.649; logoDP=9.313; NIcor=0.658; NsEucl=0.896; SSD=2.612; NSW=0.881; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=3; rNSW=1; rank_mean=1.429; match_rank=1
a	0	0	2035	506	0	0	0	17955	0	0	2166	2502	1886	0
c	0	0	4321	6406	14869	697	0	0	0	17955	0	6166	5072	0
g	0	0	2530	2792	437	0	0	0	0	0	0	6687	1598	0
t	0	0	9069	8251	2649	17258	17955	0	17955	0	15789	2600	9399	0
MA0482.1_shift3 (Gata4) 0.757 0.541 8.933 0.552 0.887 2.546 0.873 3 2 2 2 2 2 2 2.143 2
; oligos_6nt_mkv4_m4 versus MA0482.1 (Gata4); m=2/3; ncol2=11; w=10; offset=3; strand=D; shift=3; score= 2.1429; ---yCTTATCTsyy
; cor=0.757; Ncor=0.541; logoDP=8.933; NIcor=0.552; NsEucl=0.887; SSD=2.546; NSW=0.873; rcor=3; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.143; match_rank=2
a	0	0	0	10	0	0	0	2707	0	0	547	0	601	386
c	0	0	0	1039	2165	89	0	39	0	2746	0	1240	1004	929
g	0	0	0	374	306	0	0	0	0	0	0	940	157	682
t	0	0	0	1323	275	2657	2746	0	2746	0	2199	566	984	749
MA0037.2_rc_shift3 (GATA3_rc) 0.787 0.484 2.035 -0.076 0.867 2.253 0.859 1 3 3 3 3 1 3 2.429 3
; oligos_6nt_mkv4_m4 versus MA0037.2_rc (GATA3_rc); m=3/3; ncol2=8; w=8; offset=3; strand=R; shift=3; score= 2.4286; ---tYTTATCT---
; cor=0.787; Ncor=0.484; logoDP=2.035; NIcor=-0.076; NsEucl=0.867; SSD=2.253; NSW=0.859; rcor=1; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=1; rNSW=3; rank_mean=2.429; match_rank=3
a	0	0	0	0	0	0	0	4628	0	0	0	0	0	0
c	0	0	0	1120	3338	0	0	0	0	4628	0	0	0	0
g	0	0	0	712	0	0	0	0	0	0	0	0	0	0
t	0	0	0	2796	1290	4628	4628	0	4628	0	4628	0	0	0