One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.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/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 4 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NIcor |
NsEucl |
SSD |
NSW |
rcor |
rNcor |
rlogoDP |
rNIcor |
rNsEucl |
rSSD |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| positions_7nt_m1_shift0 (positions_7nt_m1) |
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; positions_7nt_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; rdgATTGTGCAATcAtt
; Alignment reference
a 23 21 11 66 0 0 3 3 0 6 74 75 5 7 52 17 18
c 17 11 10 1 0 0 0 4 0 69 0 0 8 48 10 18 17
g 22 24 43 6 0 0 71 2 75 0 0 0 5 11 6 17 16
t 13 19 11 2 75 75 1 66 0 0 1 0 57 9 7 23 24
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| MA0102.3_rc_shift2 (CEBPA_rc) |
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0.936 |
0.606 |
4.313 |
0.051 |
0.941 |
0.849 |
0.961 |
1 |
1 |
2 |
2 |
1 |
1 |
1 |
1.286 |
1 |
; positions_7nt_m1 versus MA0102.3_rc (CEBPA_rc); m=1/3; ncol2=11; w=11; offset=2; strand=R; shift=2; score= 1.2857; --krTTrTGCAAt----
; cor=0.936; Ncor=0.606; logoDP=4.313; NIcor=0.051; NsEucl=0.941; SSD=0.849; NSW=0.961; rcor=1; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
a 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0
c 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0
g 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0
t 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0
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| MA0466.1_rc_shift3 (CEBPB_rc) |
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0.919 |
0.594 |
2.935 |
-0.034 |
0.934 |
1.053 |
0.952 |
2 |
2 |
3 |
3 |
2 |
2 |
2 |
2.286 |
2 |
; positions_7nt_m1 versus MA0466.1_rc (CEBPB_rc); m=2/3; ncol2=11; w=11; offset=3; strand=R; shift=3; score= 2.2857; ---rTkrTGCAATm---
; cor=0.919; Ncor=0.594; logoDP=2.935; NIcor=-0.034; NsEucl=0.934; SSD=1.053; NSW=0.952; rcor=2; rNcor=2; rlogoDP=3; rNIcor=3; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.286; match_rank=2
a 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0
c 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0
g 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0
t 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0
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| MA0078.1_shift0 (Sox17) |
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0.824 |
0.436 |
7.119 |
0.442 |
0.907 |
1.416 |
0.921 |
3 |
3 |
1 |
1 |
3 |
3 |
3 |
2.429 |
3 |
; positions_7nt_m1 versus MA0078.1 (Sox17); m=3/3; ncol2=9; w=9; offset=0; strand=D; shift=0; score= 2.4286; yhyATTGTs--------
; cor=0.824; Ncor=0.436; logoDP=7.119; NIcor=0.442; NsEucl=0.907; SSD=1.416; NSW=0.921; rcor=3; rNcor=3; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.429; match_rank=3
a 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 0 0
c 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 0 0
g 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 0 0
t 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0 0 0
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