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.2025-05-16.175823_2025-05-16.175823_YJjJog/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2.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.2025-05-16.175823_2025-05-16.175823_YJjJog/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift1 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2) |
 |
|
|
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=14; shift=1; ncol=15; -rwtgAATGAATGra
; Alignment reference
a 0 25 28 13 14 62 68 3 4 68 64 1 4 32 25
c 0 11 12 6 9 3 3 3 2 3 2 1 1 11 18
g 0 27 15 15 43 3 4 2 68 4 8 4 70 21 15
t 0 13 21 42 10 8 1 68 2 1 2 70 1 12 18
|
| MA1124.1_rc_shift0 (ZNF24_rc) |
 |
|
|
; oligos_7nt_mkv2_m2 versus MA1124.1_rc (ZNF24_rc); m=1/2; ncol2=13; w=-1; offset=-1; strand=R; shift=0; score=0.72788; GAATGAATGAATG--
; cor=; Ncor=
a 2685.0 19146.0 19421.0 279.0 789.0 22610.0 22192.0 147.0 723.0 21867.0 19505.0 1493.0 2848.0 0 0
c 856.0 1045.0 811.0 589.0 93.0 182.0 128.0 501.0 118.0 461.0 739.0 1967.0 1345.0 0 0
g 17701.0 2128.0 2062.0 402.0 22068.0 330.0 887.0 219.0 22137.0 544.0 2102.0 1816.0 17056.0 0 0
t 2062.0 985.0 1010.0 22034.0 354.0 182.0 97.0 22437.0 326.0 432.0 958.0 18028.0 2055.0 0 0
|
| MA1530.2_rc_shift7 (NKX6-3_rc) |
 |
|
|
; oligos_7nt_mkv2_m2 versus MA1530.2_rc (NKX6-3_rc); m=2/2; ncol2=8; w=0; offset=6; strand=R; shift=7; score= 0.4053; -------wTAATGrs
; cor=; Ncor=
a 0 0 0 0 0 0 0 3753.0 0.0 6906.0 6906.0 0.0 626.0 6906.0 51.0
c 0 0 0 0 0 0 0 379.0 701.0 0.0 0.0 0.0 533.0 0.0 2723.0
g 0 0 0 0 0 0 0 789.0 0.0 467.0 0.0 0.0 6753.0 4562.0 2731.0
t 0 0 0 0 0 0 0 6906.0 6906.0 0.0 0.0 6906.0 153.0 0.0 1400.0
|