One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125527_2026-01-05.125527_ogDb5d/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_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/2026/01/05/peak-motifs.2026-01-05.125527_2026-01-05.125527_ogDb5d/results/discovered_motifs/oligos_6nt_mkv4_m3/peak-motifs_oligos_6nt_mkv4_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift3 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv4_m3_shift3 (oligos_6nt_mkv4_m3) |
 |
|
|
; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=3; ncol=13; ---ssCGGCCGss
; Alignment reference
a 0 0 0 4509 4870 250 351 978 1754 268 576 3846 4128
c 0 0 0 17107 9705 34881 5715 3792 30330 30520 1147 18433 11110
g 0 0 0 11110 18433 1147 30520 30330 3792 5715 34881 9705 17107
t 0 0 0 4128 3846 576 268 1754 978 351 250 4870 4509
|
| MA0131.3_rc_shift4 (HINFP_rc) |
 |
|
|
; oligos_6nt_mkv4_m3 versus MA0131.3_rc (HINFP_rc); m=1/2; ncol2=8; w=0; offset=1; strand=R; shift=4; score=0.583634; ----GCGGACGy-
; cor=; Ncor=
a 0 0 0 0 12.0 21.0 3.0 0.0 470.0 10.0 7.0 17.0 0
c 0 0 0 0 15.0 472.0 0.0 13.0 0.0 484.0 97.0 217.0 0
g 0 0 0 0 395.0 31.0 413.0 404.0 0.0 14.0 388.0 45.0 0
t 0 0 0 0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 276.0 0
|
| MA1721.2_shift0 (ZNF93) |
 |
|
|
; oligos_6nt_mkv4_m3 versus MA1721.2 (ZNF93); m=2/2; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score=0.51061; gGyrkCrGCAGCG
; cor=; Ncor=
a 467.0 175.0 117.0 1455.0 61.0 38.0 1001.0 18.0 23.0 1659.0 30.0 19.0 340.0
c 279.0 233.0 1120.0 177.0 114.0 2278.0 92.0 26.0 2279.0 96.0 20.0 2292.0 138.0
g 1499.0 1857.0 211.0 663.0 1483.0 22.0 1263.0 2334.0 42.0 576.0 2328.0 33.0 1784.0
t 143.0 123.0 940.0 93.0 730.0 50.0 32.0 10.0 44.0 57.0 10.0 44.0 126.0
|