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.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_6nt_mkv1_m3/peak-motifs_oligos_6nt_mkv1_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.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_6nt_mkv1_m3/peak-motifs_oligos_6nt_mkv1_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift0 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3) |
 |
|
|
; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; msAGACACACacm
; Alignment reference
a 8 3 16 0 18 0 17 0 18 1 7 2 5
c 5 6 1 2 0 14 0 18 0 16 3 12 5
g 2 6 1 15 0 3 1 0 0 1 4 4 4
t 3 3 0 1 0 1 0 0 0 0 4 0 4
|
| MA1107.3_shift3 (KLF9) |
 |
|
|
; oligos_6nt_mkv1_m3 versus MA1107.3 (KLF9); m=1/2; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.527755; ---gCCACACCCA
; cor=; Ncor=
a 0 0 0 2862.0 4664.0 287.0 21899.0 221.0 19187.0 224.0 2428.0 146.0 18837.0
c 0 0 0 4342.0 17839.0 24709.0 2559.0 24863.0 1070.0 24365.0 22117.0 24682.0 4339.0
g 0 0 0 16852.0 1660.0 291.0 708.0 353.0 4340.0 735.0 605.0 205.0 852.0
t 0 0 0 1523.0 1416.0 292.0 413.0 142.0 982.0 255.0 429.0 546.0 1551.0
|
| MA1153.2_rc_shift0 (Smad4_rc) |
 |
|
|
; oligos_6nt_mkv1_m3 versus MA1153.2_rc (Smad4_rc); m=2/2; ncol2=7; w=0; offset=0; strand=R; shift=0; score=0.438205; CyAGACr------
; cor=; Ncor=
a 0.0 0.0 1000.0 0.0 1000.0 0.0 581.0 0 0 0 0 0 0
c 1000.0 404.0 0.0 0.0 0.0 1000.0 81.0 0 0 0 0 0 0
g 0.0 0.0 0.0 1000.0 0.0 0.0 250.0 0 0 0 0 0 0
t 0.0 596.0 0.0 0.0 0.0 0.0 88.0 0 0 0 0 0 0
|