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_6nt_m1/peak-motifs_positions_6nt_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_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_6nt_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_6nt_m1_shift0 (positions_6nt_m1) |
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; positions_6nt_m1; m=0 (reference); ncol1=18; shift=0; ncol=18; aakgATTGTGCAATcawt
; Alignment reference
a 18 18 9 6 48 1 0 3 2 0 4 54 55 3 6 36 14 13
c 13 13 7 6 2 0 0 0 3 0 51 0 0 3 36 9 12 9
g 12 13 14 30 4 0 0 52 2 55 0 0 0 1 5 6 11 13
t 12 11 25 13 1 54 55 0 48 0 0 1 0 48 8 4 18 20
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| MA0102.3_rc_shift3 (CEBPA_rc) |
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0.938 |
0.573 |
4.109 |
0.042 |
0.941 |
0.852 |
0.961 |
1 |
1 |
2 |
2 |
1 |
1 |
1 |
1.286 |
1 |
; positions_6nt_m1 versus MA0102.3_rc (CEBPA_rc); m=1/3; ncol2=11; w=11; offset=3; strand=R; shift=3; score= 1.2857; ---krTTrTGCAAt----
; cor=0.938; Ncor=0.573; logoDP=4.109; NIcor=0.042; NsEucl=0.941; SSD=0.852; 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 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0
c 0 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0
g 0 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0
t 0 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0
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| MA0466.1_rc_shift4 (CEBPB_rc) |
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0.920 |
0.562 |
2.945 |
-0.032 |
0.934 |
1.069 |
0.951 |
2 |
2 |
3 |
3 |
2 |
2 |
2 |
2.286 |
2 |
; positions_6nt_m1 versus MA0466.1_rc (CEBPB_rc); m=2/3; ncol2=11; w=11; offset=4; strand=R; shift=4; score= 2.2857; ----rTkrTGCAATm---
; cor=0.920; Ncor=0.562; logoDP=2.945; NIcor=-0.032; NsEucl=0.934; SSD=1.069; NSW=0.951; 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 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0
c 0 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0
g 0 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0
t 0 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0
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| MA0078.1_shift1 (Sox17) |
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0.828 |
0.414 |
6.943 |
0.418 |
0.908 |
1.372 |
0.924 |
3 |
3 |
1 |
1 |
3 |
3 |
3 |
2.429 |
3 |
; positions_6nt_m1 versus MA0078.1 (Sox17); m=3/3; ncol2=9; w=9; offset=1; strand=D; shift=1; score= 2.4286; -yhyATTGTs--------
; cor=0.828; Ncor=0.414; logoDP=6.943; NIcor=0.418; NsEucl=0.908; SSD=1.372; NSW=0.924; rcor=3; rNcor=3; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.429; match_rank=3
a 0 7 8 3 30 0 0 0 0 0 0 0 0 0 0 0 0 0
c 0 9 8 18 0 1 0 0 0 17 0 0 0 0 0 0 0 0
g 0 6 4 1 0 0 0 31 2 10 0 0 0 0 0 0 0 0
t 0 9 11 9 1 30 31 0 29 4 0 0 0 0 0 0 0 0
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