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_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_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.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/oligos_8nt_mkv6_m4/peak-motifs_oligos_8nt_mkv6_m4_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m4_shift1 ; 8 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_8nt_mkv6_m4_shift1 (oligos_8nt_mkv6_m4)                                
; oligos_8nt_mkv6_m4; m=0 (reference); ncol1=13; shift=1; ncol=14; -wrTTACACAATah
; Alignment reference
a	0	714	1247	9	3	2479	2	1960	1	2463	2478	125	915	663
c	0	367	375	3	0	0	2486	7	2449	4	2	391	571	645
g	0	555	662	8	10	10	2	516	0	21	8	175	399	404
t	0	862	214	2478	2485	9	8	15	48	10	10	1807	613	786
MA0043.1_shift1 (HLF) 0.859 0.793 6.302 0.770 0.926 1.585 0.934 1 1 3 1 1 2 1 1.429 1
; oligos_8nt_mkv6_m4 versus MA0043.1 (HLF); m=1/7; ncol2=12; w=12; offset=0; strand=D; shift=1; score= 1.4286; -krTTACryAAth-
; cor=0.859; Ncor=0.793; logoDP=6.302; NIcor=0.770; NsEucl=0.926; SSD=1.585; NSW=0.934; rcor=1; rNcor=1; rlogoDP=3; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.429; match_rank=1
a	0	1	6	1	0	13	0	6	0	13	15	2	5	0
c	0	4	0	0	0	1	15	0	9	4	0	3	5	0
g	0	8	12	0	3	2	1	12	0	1	1	1	3	0
t	0	5	0	17	15	2	2	0	9	0	2	12	5	0
MA0102.3_shift2 (CEBPA) 0.809 0.685 9.041 0.680 0.907 2.099 0.905 5 2 1 2 3 6 4 3.286 2
; oligos_8nt_mkv6_m4 versus MA0102.3 (CEBPA); m=2/7; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 3.2857; --aTTGCAyAAym-
; cor=0.809; Ncor=0.685; logoDP=9.041; NIcor=0.680; NsEucl=0.907; SSD=2.099; NSW=0.905; rcor=5; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=3; rSSD=6; rNSW=4; rank_mean=3.286; match_rank=2
a	0	0	10351	0	0	705	0	11956	2660	12226	15318	0	5804	0
c	0	0	1332	0	0	0	15318	1274	7654	3092	0	5688	4963	0
g	0	0	3635	0	0	11304	0	1066	0	0	0	1804	890	0
t	0	0	0	15318	15318	3309	0	1022	5004	0	0	7826	3661	0
MA0102.1_shift3 (Cebpa) 0.808 0.634 6.273 0.611 0.908 2.063 0.906 6 4 4 4 2 5 3 4.000 3
; oligos_8nt_mkv6_m4 versus MA0102.1 (Cebpa); m=3/7; ncol2=12; w=11; offset=2; strand=D; shift=3; score=      4; ---TtkygCAAyvy
; cor=0.808; Ncor=0.634; logoDP=6.273; NIcor=0.611; NsEucl=0.908; SSD=2.063; NSW=0.906; rcor=6; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=2; rSSD=5; rNSW=3; rank_mean=4.000; match_rank=3
a	0	0	0	3	1	4	2	4	2	18	18	0	5	2
c	0	0	0	0	1	1	9	2	15	0	0	6	6	5
g	0	0	0	0	4	6	2	10	0	0	0	2	5	3
t	0	0	0	15	12	7	5	2	1	0	0	10	2	8
MA0078.1_rc_shift6 (Sox17_rc) 0.840 0.480 2.389 0.159 0.903 1.211 0.924 2 7 6 6 4 1 2 4.000 4
; oligos_8nt_mkv6_m4 versus MA0078.1_rc (Sox17_rc); m=4/7; ncol2=9; w=8; offset=5; strand=R; shift=6; score=      4; ------sACAATrd
; cor=0.840; Ncor=0.480; logoDP=2.389; NIcor=0.159; NsEucl=0.903; SSD=1.211; NSW=0.924; rcor=2; rNcor=7; rlogoDP=6; rNIcor=6; rNsEucl=4; rSSD=1; rNSW=2; rank_mean=4.000; match_rank=4
a	0	0	0	0	0	0	4	29	0	31	30	1	9	11
c	0	0	0	0	0	0	10	2	31	0	0	0	1	4
g	0	0	0	0	0	0	17	0	0	0	1	0	18	8
t	0	0	0	0	0	0	0	0	0	0	0	30	3	8
MA0466.1_shift1 (CEBPB) 0.784 0.664 8.817 0.654 0.901 2.375 0.892 7 3 2 3 5 7 6 4.714 5
; oligos_8nt_mkv6_m4 versus MA0466.1 (CEBPB); m=5/7; ncol2=11; w=11; offset=0; strand=D; shift=1; score= 4.7143; -kATTGCAymAy--
; cor=0.784; Ncor=0.664; logoDP=8.817; NIcor=0.654; NsEucl=0.901; SSD=2.375; NSW=0.892; rcor=7; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=5; rSSD=7; rNSW=6; rank_mean=4.714; match_rank=5
a	0	13006	75198	0	0	4556	0	74715	8654	60151	99494	0	0	0
c	0	10026	5868	0	0	0	99494	5478	51954	39343	0	36038	0	0
g	0	33617	18428	0	0	75531	0	10015	0	0	0	2043	0	0
t	0	42845	0	99494	99494	19407	0	9286	38886	0	0	61413	0	0
MA0102.2_shift3 (CEBPA) 0.818 0.566 6.271 0.538 0.890 1.971 0.890 3 6 5 5 7 3 7 5.143 6
; oligos_8nt_mkv6_m4 versus MA0102.2 (CEBPA); m=6/7; ncol2=9; w=9; offset=2; strand=D; shift=3; score= 5.1429; ---TtkygCAAy--
; cor=0.818; Ncor=0.566; logoDP=6.271; NIcor=0.538; NsEucl=0.890; SSD=1.971; NSW=0.890; rcor=3; rNcor=6; rlogoDP=5; rNIcor=5; rNsEucl=7; rSSD=3; rNSW=7; rank_mean=5.143; match_rank=6
a	0	0	0	3	1	4	2	4	2	18	18	0	0	0
c	0	0	0	0	1	1	9	2	15	0	0	6	0	0
g	0	0	0	0	4	6	2	10	0	0	0	2	0	0
t	0	0	0	15	12	7	5	2	1	0	0	10	0	0
MA0025.1_rc_shift0 (NFIL3_rc) 0.813 0.581 1.794 0.055 0.899 2.027 0.899 4 5 7 7 6 4 5 5.429 7
; oligos_8nt_mkv6_m4 versus MA0025.1_rc (NFIL3_rc); m=7/7; ncol2=11; w=10; offset=-1; strand=R; shift=0; score= 5.4286; ayrTTACrTAA---
; cor=0.813; Ncor=0.581; logoDP=1.794; NIcor=0.055; NsEucl=0.899; SSD=2.027; NSW=0.899; rcor=4; rNcor=5; rlogoDP=7; rNIcor=7; rNsEucl=6; rSSD=4; rNSW=5; rank_mean=5.429; match_rank=7
a	10	4	8	0	0	23	0	15	1	21	22	0	0	0
c	3	7	4	1	0	0	21	0	0	2	0	0	0	0
g	5	5	11	0	0	0	0	8	0	0	0	0	0	0
t	5	7	0	22	23	0	2	0	22	0	1	0	0	0