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_m5/peak-motifs_positions_6nt_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_6nt_m5/peak-motifs_positions_6nt_m5_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift0 ; 3 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_m5_shift0 (positions_6nt_m5) |
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; positions_6nt_m5; m=0 (reference); ncol1=16; shift=0; ncol=16; aktgATTGCACAACay
; Alignment reference
a 31 15 18 11 69 0 0 2 0 74 0 79 79 1 30 14
c 15 19 7 10 2 0 0 1 79 1 74 0 0 57 17 28
g 16 23 9 48 7 0 0 74 0 4 0 0 0 5 13 11
t 17 22 45 10 1 79 79 2 0 0 5 0 0 16 19 26
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| MA0102.3_shift4 (CEBPA) |
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0.941 |
0.647 |
10.317 |
0.636 |
0.943 |
0.792 |
0.964 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_6nt_m5 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=4; strand=D; shift=4; score= 1; ----aTTGCAyAAym-
; cor=0.941; Ncor=0.647; logoDP=10.317; NIcor=0.636; NsEucl=0.943; SSD=0.792; NSW=0.964; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0
c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0
g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0
t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
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| MA0466.1_shift3 (CEBPB) |
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0.907 |
0.623 |
10.152 |
0.609 |
0.930 |
1.201 |
0.945 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; positions_6nt_m5 versus MA0466.1 (CEBPB); m=2/2; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 2; ---kATTGCAymAy--
; cor=0.907; Ncor=0.623; logoDP=10.152; NIcor=0.609; NsEucl=0.930; SSD=1.201; NSW=0.945; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0
c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0
g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0
t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
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