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/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3.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/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_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 |
|---|
| oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3) |
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; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; rwkATTTCACAAym
; Alignment reference
a 62 57 19 194 1 5 23 0 176 9 201 195 25 70
c 40 46 26 4 0 1 5 210 12 190 4 1 64 58
g 69 41 101 10 2 9 33 0 15 2 0 8 32 39
t 39 66 64 2 207 195 149 0 7 9 5 6 89 43
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| MA0102.3_shift3 (CEBPA) |
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0.895 |
0.703 |
8.236 |
0.685 |
0.933 |
1.078 |
0.951 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_7nt_mkv4_m3 versus MA0102.3 (CEBPA); m=1/2; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 1; ---aTTGCAyAAym
; cor=0.895; Ncor=0.703; logoDP=8.236; NIcor=0.685; NsEucl=0.933; SSD=1.078; NSW=0.951; 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 10351 0 0 705 0 11956 2660 12226 15318 0 5804
c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963
g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890
t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661
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| MA0466.1_shift2 (CEBPB) |
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0.870 |
0.684 |
8.100 |
0.661 |
0.925 |
1.355 |
0.938 |
2 |
2 |
2 |
2 |
2 |
2 |
2 |
2.000 |
2 |
; oligos_7nt_mkv4_m3 versus MA0466.1 (CEBPB); m=2/2; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 2; --kATTGCAymAy-
; cor=0.870; Ncor=0.684; logoDP=8.100; NIcor=0.661; NsEucl=0.925; SSD=1.355; NSW=0.938; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0
c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0
g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0
t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0
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