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_m5/peak-motifs_positions_7nt_m5.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_m5/peak-motifs_positions_7nt_m5_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_7nt_m5_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_m5_shift0 (positions_7nt_m5) |
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; positions_7nt_m5; m=0 (reference); ncol1=18; shift=0; ncol=18; gwgATTGTGCAACAchkr
; Alignment reference
a 11 18 8 49 0 0 1 3 0 1 53 54 2 42 5 22 12 18
c 13 7 12 3 0 0 0 3 0 50 1 0 41 7 29 15 6 11
g 21 10 29 1 0 0 53 2 54 1 0 0 5 2 10 3 17 15
t 9 19 5 1 54 54 0 46 0 2 0 0 6 3 10 14 19 10
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| MA0102.3_rc_shift2 (CEBPA_rc) |
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0.873 |
0.534 |
4.210 |
0.055 |
0.920 |
1.563 |
0.929 |
1 |
1 |
2 |
2 |
1 |
2 |
1 |
1.429 |
1 |
; positions_7nt_m5 versus MA0102.3_rc (CEBPA_rc); m=1/3; ncol2=11; w=11; offset=2; strand=R; shift=2; score= 1.4286; --krTTrTGCAAt-----
; cor=0.873; Ncor=0.534; logoDP=4.210; NIcor=0.055; NsEucl=0.920; SSD=1.563; NSW=0.929; rcor=1; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.429; match_rank=1
a 0 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0 0
c 0 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0 0
g 0 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0 0
t 0 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0 0
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| MA0078.1_shift0 (Sox17) |
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0.839 |
0.420 |
7.380 |
0.423 |
0.910 |
1.307 |
0.927 |
3 |
3 |
1 |
1 |
3 |
1 |
2 |
2.000 |
2 |
; positions_7nt_m5 versus MA0078.1 (Sox17); m=2/3; ncol2=9; w=9; offset=0; strand=D; shift=0; score= 2; yhyATTGTs---------
; cor=0.839; Ncor=0.420; logoDP=7.380; NIcor=0.423; NsEucl=0.910; SSD=1.307; NSW=0.927; rcor=3; rNcor=3; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=1; rNSW=2; rank_mean=2.000; match_rank=2
a 7 8 3 30 0 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 0
g 6 4 1 0 0 0 31 2 10 0 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 0
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| MA0466.1_rc_shift3 (CEBPB_rc) |
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0.852 |
0.521 |
2.820 |
-0.035 |
0.912 |
1.869 |
0.915 |
2 |
2 |
3 |
3 |
2 |
3 |
3 |
2.571 |
3 |
; positions_7nt_m5 versus MA0466.1_rc (CEBPB_rc); m=3/3; ncol2=11; w=11; offset=3; strand=R; shift=3; score= 2.5714; ---rTkrTGCAATm----
; cor=0.852; Ncor=0.521; logoDP=2.820; NIcor=-0.035; NsEucl=0.912; SSD=1.869; NSW=0.915; rcor=2; rNcor=2; rlogoDP=3; rNIcor=3; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.571; match_rank=3
a 0 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 0
c 0 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 0
g 0 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 0
t 0 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0 0
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