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.2026-01-05.052000_2026-01-05.052000_2qIqyX/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_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/2026/01/05/peak-motifs.2026-01-05.052000_2026-01-05.052000_2qIqyX/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift0 ; 7 matrices ; sort_field=Ncor

Matrix nameAligned logoscor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)     
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; hrgACAAGTCys
; Alignment reference
a	146	198	81	397	7	556	404	5	11	18	140	141
c	168	70	59	44	557	11	24	7	16	535	202	157
g	108	209	350	116	12	9	15	560	6	6	54	172
t	159	104	91	24	5	5	138	9	548	22	185	111
MA0844.2_shift2 (XBP1) 
; oligos_6nt_mkv3_m2 versus MA0844.2 (XBP1); m=1/6; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.559066; --GmCACGTCAk
; cor=; Ncor=
a	0	0	974.0	3699.0	167.0	7840.0	9.0	52.0	0.0	380.0	8004.0	230.0
c	0	0	367.0	3809.0	7169.0	17.0	7356.0	0.0	16.0	7264.0	48.0	2273.0
g	0	0	9168.0	59.0	222.0	276.0	2.0	11353.0	8.0	47.0	173.0	3157.0
t	0	0	2321.0	247.0	442.0	118.0	10.0	10.0	9107.0	35.0	92.0	6389.0
MA0676.1_shift3 (Nr2e1) 
; oligos_6nt_mkv3_m2 versus MA0676.1 (Nr2e1); m=2/6; ncol2=9; w=0; offset=3; strand=D; shift=3; score=0.525572; ---aaAAGTCAA
; cor=; Ncor=
a	0	0	0	1118.0	1118.0	1118.0	1118.0	40.0	0.0	11.0	1118.0	1118.0
c	0	0	0	244.0	89.0	1.0	0.0	0.0	58.0	1118.0	0.0	131.0
g	0	0	0	191.0	448.0	101.0	74.0	1118.0	0.0	12.0	0.0	117.0
t	0	0	0	401.0	369.0	19.0	5.0	8.0	1118.0	112.0	0.0	247.0
MA0861.2_shift3 (TP73) 
; oligos_6nt_mkv3_m2 versus MA0861.2 (TP73); m=3/6; ncol2=16; w=0; offset=3; strand=D; shift=3; score=0.431617; ---rCATGTcyr
; cor=; Ncor=
a	0	0	0	6206.0	0.0	8760.0	3837.0	8.0	130.0	1377.0	2166.0	3488.0
c	0	0	0	429.0	10829.0	124.0	293.0	28.0	2591.0	8161.0	2940.0	2418.0
g	0	0	0	3304.0	0.0	557.0	806.0	11787.0	91.0	783.0	2230.0	3558.0
t	0	0	0	208.0	0.0	198.0	11480.0	1.0	11892.0	2749.0	4242.0	2457.0
MA0525.2_rc_shift2 (TP63_rc) 
; oligos_6nt_mkv3_m2 versus MA0525.2_rc (TP63_rc); m=4/6; ncol2=18; w=0; offset=2; strand=R; shift=2; score=0.416263; --gACATGTymc
; cor=; Ncor=
a	0	0	606.0	3126.0	0.0	2823.0	192.0	0.0	45.0	47.0	829.0	13.0
c	0	0	198.0	1.0	3532.0	8.0	1.0	0.0	48.0	2132.0	1656.0	2070.0
g	0	0	2099.0	202.0	0.0	617.0	0.0	2788.0	0.0	1.0	681.0	478.0
t	0	0	701.0	49.0	0.0	75.0	2151.0	0.0	2192.0	993.0	112.0	649.0
MA0775.2_shift0 (MEIS3) 
; oligos_6nt_mkv3_m2 versus MA0775.2 (MEIS3); m=5/6; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.413672; wTGACAg-----
; cor=; Ncor=
a	1866.0	465.0	0.0	7165.0	53.0	7165.0	1690.0	0	0	0	0	0
c	60.0	383.0	6.0	20.0	7165.0	8.0	1889.0	0	0	0	0	0
g	1788.0	260.0	7165.0	455.0	8.0	468.0	7165.0	0	0	0	0	0
t	3451.0	7165.0	0.0	53.0	160.0	145.0	2094.0	0	0	0	0	0
MA0161.3_rc_shift1 (NFIC_rc) 
; oligos_6nt_mkv3_m2 versus MA0161.3_rc (NFIC_rc); m=6/6; ncol2=7; w=0; offset=1; strand=R; shift=1; score=0.412971; -TGCCAAG----
; cor=; Ncor=
a	0	574.0	530.0	290.0	81.0	10745.0	10781.0	324.0	0	0	0	0
c	0	478.0	88.0	10973.0	11087.0	177.0	369.0	329.0	0	0	0	0
g	0	397.0	10725.0	121.0	129.0	333.0	303.0	10542.0	0	0	0	0
t	0	10158.0	264.0	223.0	310.0	352.0	154.0	412.0	0	0	0	0