One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.175219_2025-05-16.175219_UyZibC/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.175219_2025-05-16.175219_UyZibC/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift2 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3) |
 |
|
|
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwTATATATAww
; Alignment reference
a 0 0 36 33 9 64 4 65 0 58 1 52 22 19
c 0 0 6 4 3 0 1 1 0 3 1 2 7 5
g 0 0 5 7 2 1 3 0 1 1 0 3 4 6
t 0 0 19 22 52 1 58 0 65 4 64 9 33 36
|
| MA0108.3_shift6 (TBP) |
 |
|
|
; oligos_7nt_mkv2_m3 versus MA0108.3 (TBP); m=1/2; ncol2=7; w=0; offset=4; strand=D; shift=6; score=0.495954; ------TATAWAw-
; cor=; Ncor=
a 0 0 0 0 0 0 16.0 352.0 3.0 354.0 268.0 360.0 222.0 0
c 0 0 0 0 0 0 46.0 0.0 10.0 0.0 0.0 3.0 2.0 0
g 0 0 0 0 0 0 18.0 2.0 2.0 5.0 0.0 20.0 44.0 0
t 0 0 0 0 0 0 309.0 35.0 374.0 30.0 121.0 6.0 121.0 0
|
| MA1974.2_rc_shift0 (ZNF211_rc) |
 |
|
|
; oligos_7nt_mkv2_m3 versus MA1974.2_rc (ZNF211_rc); m=2/2; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.411296; rTGGTATATr----
; cor=; Ncor=
a 412.0 41.0 38.0 8.0 7.0 776.0 2.0 769.0 3.0 393.0 0 0 0 0
c 44.0 20.0 5.0 7.0 6.0 3.0 7.0 5.0 13.0 83.0 0 0 0 0
g 262.0 21.0 741.0 776.0 7.0 11.0 4.0 17.0 21.0 275.0 0 0 0 0
t 76.0 712.0 10.0 3.0 774.0 4.0 781.0 3.0 757.0 43.0 0 0 0 0
|