One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_8nt_test_vs_ctrl_m2/peak-motifs_oligos_8nt_test_vs_ctrl_m2.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/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_8nt_test_vs_ctrl_m2/peak-motifs_oligos_8nt_test_vs_ctrl_m2_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_8nt_test_vs_ctrl_m2_shift0 ; 6 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_test_vs_ctrl_m2_shift0 (oligos_8nt_test_vs_ctrl_m2)                                
; oligos_8nt_test_vs_ctrl_m2; m=0 (reference); ncol1=23; shift=0; ncol=23; myTCCArrGmCCAAAGGkCAGvh
; Alignment reference
a	2	0	0	0	0	3	2	2	0	2	0	0	3	3	3	0	0	0	0	3	0	1	1
c	1	2	0	3	3	0	0	0	0	1	3	3	0	0	0	0	0	0	3	0	0	1	1
g	0	0	0	0	0	0	1	1	3	0	0	0	0	0	0	3	3	1	0	0	3	1	0
t	0	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	1
MA0512.1_shift11 (Rxra) 0.905 0.433 10.330 0.424 0.925 1.352 0.939 1 5 1 3 1 1 1 1.857 1
; oligos_8nt_test_vs_ctrl_m2 versus MA0512.1 (Rxra); m=1/5; ncol2=11; w=11; offset=11; strand=D; shift=11; score= 1.8571; -----------CArAGKTCAgd-
; cor=0.905; Ncor=0.433; logoDP=10.330; NIcor=0.424; NsEucl=0.925; SSD=1.352; NSW=0.939; rcor=1; rNcor=5; rlogoDP=1; rNIcor=3; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.857; match_rank=1
a	0	0	0	0	0	0	0	0	0	0	0	278	4154	2623	4877	0	0	0	0	5348	1150	1640	0
c	0	0	0	0	0	0	0	0	0	0	0	4521	418	252	0	0	0	583	5348	0	1070	742	0
g	0	0	0	0	0	0	0	0	0	0	0	305	9	2473	471	5348	3882	643	0	0	2336	1569	0
t	0	0	0	0	0	0	0	0	0	0	0	244	767	0	0	0	1466	4122	0	0	792	1397	0
MA0484.1_shift5 (HNF4G) 0.818 0.534 10.149 0.530 0.916 3.212 0.893 3 1 2 1 2 4 4 2.429 2
; oligos_8nt_test_vs_ctrl_m2 versus MA0484.1 (HNF4G); m=2/5; ncol2=15; w=15; offset=5; strand=D; shift=5; score= 2.4286; -----arrGkyCAAAGkyCA---
; cor=0.818; Ncor=0.534; logoDP=10.149; NIcor=0.530; NsEucl=0.916; SSD=3.212; NSW=0.893; rcor=3; rNcor=1; rlogoDP=2; rNIcor=1; rNsEucl=2; rSSD=4; rNSW=4; rank_mean=2.429; match_rank=2
a	0	0	0	0	0	3514	3259	4696	1103	1944	1511	0	9343	7889	8464	99	324	225	159	6785	0	0	0
c	0	0	0	0	0	1864	1531	102	201	713	2870	8827	55	82	0	6	143	4338	8377	794	0	0	0
g	0	0	0	0	0	2011	3830	3811	7480	3301	2279	221	54	1481	938	9098	3624	1107	85	556	0	0	0
t	0	0	0	0	0	2063	832	843	668	3494	2792	404	0	0	50	249	5361	3782	831	1317	0	0	0
MA0114.1_shift7 (HNF4A) 0.862 0.487 6.666 0.497 0.914 2.491 0.904 2 4 3 2 3 2 2 2.571 3
; oligos_8nt_test_vs_ctrl_m2 versus MA0114.1 (HNF4A); m=3/5; ncol2=13; w=13; offset=7; strand=D; shift=7; score= 2.5714; -------rGgbCAAAGkyCa---
; cor=0.862; Ncor=0.487; logoDP=6.666; NIcor=0.497; NsEucl=0.914; SSD=2.491; NSW=0.904; rcor=2; rNcor=4; rlogoDP=3; rNIcor=2; rNsEucl=3; rSSD=2; rNSW=2; rank_mean=2.571; match_rank=3
a	0	0	0	0	0	0	0	28	2	12	5	3	59	53	56	4	6	3	4	42	0	0	0
c	0	0	0	0	0	0	0	7	2	4	23	51	1	2	1	4	2	22	49	7	0	0	0
g	0	0	0	0	0	0	0	27	56	35	20	4	3	10	8	58	33	11	5	10	0	0	0
t	0	0	0	0	0	0	0	5	7	16	19	9	4	2	2	1	26	31	9	8	0	0	0
MA0017.1_rc_shift6 (NR2F1_rc) 0.817 0.497 3.603 -0.066 0.914 2.905 0.896 4 3 5 5 4 3 3 3.857 4
; oligos_8nt_test_vs_ctrl_m2 versus MA0017.1_rc (NR2F1_rc); m=4/5; ncol2=14; w=14; offset=6; strand=R; shift=6; score= 3.8571; ------arGkkCAAAGkTCA---
; cor=0.817; Ncor=0.497; logoDP=3.603; NIcor=-0.066; NsEucl=0.914; SSD=2.905; NSW=0.896; rcor=4; rNcor=3; rlogoDP=5; rNIcor=5; rNsEucl=4; rSSD=3; rNSW=3; rank_mean=3.857; match_rank=4
a	0	0	0	0	0	0	7	4	1	1	0	0	12	11	10	0	0	0	0	11	0	0	0
c	0	0	0	0	0	0	3	0	1	1	3	11	0	0	0	0	0	1	12	2	0	0	0
g	0	0	0	0	0	0	3	6	10	5	4	0	0	2	3	13	7	0	0	0	0	0	0
t	0	0	0	0	0	0	0	3	1	6	6	2	1	0	0	0	6	12	1	0	0	0	0
MA0114.2_rc_shift6 (HNF4A_rc) 0.795 0.519 5.945 0.175 0.912 3.514 0.883 5 2 4 4 5 5 5 4.286 5
; oligos_8nt_test_vs_ctrl_m2 versus MA0114.2_rc (HNF4A_rc); m=5/5; ncol2=15; w=15; offset=6; strand=R; shift=6; score= 4.2857; ------rrGkyCAAAGkyCAg--
; cor=0.795; Ncor=0.519; logoDP=5.945; NIcor=0.175; NsEucl=0.912; SSD=3.514; NSW=0.883; rcor=5; rNcor=2; rlogoDP=4; rNIcor=4; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=4.286; match_rank=5
a	0	0	0	0	0	0	5247	7985	1769	3334	2413	128	16188	13586	15112	49	988	477	70	13410	4057	0	0
c	0	0	0	0	0	0	3001	415	352	1662	5340	15741	407	367	0	67	329	8370	15810	907	3974	0	0
g	0	0	0	0	0	0	6450	6498	13491	5653	3745	35	173	2637	1630	16535	4425	1846	51	720	5971	0	0
t	0	0	0	0	0	0	2070	1870	1156	6119	5270	864	0	178	26	117	11026	6075	837	1731	2766	0	0