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/positions_7nt_m3/peak-motifs_positions_7nt_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.2026-01-05.052000_2026-01-05.052000_2qIqyX/results/discovered_motifs/positions_7nt_m3/peak-motifs_positions_7nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift6 ; 5 matrices ; sort_field=Ncor

Matrix nameAligned logoscor Ncor Aligned matrices
positions_7nt_m3_shift6 (positions_7nt_m3)     
; positions_7nt_m3; m=0 (reference); ncol1=16; shift=6; ncol=22; ------yyCAGACATGTCTGrr
; Alignment reference
a	0	0	0	0	0	0	35	58	37	231	15	234	7	289	15	2	6	11	22	38	82	124
c	0	0	0	0	0	0	120	124	221	11	7	5	306	8	4	1	71	283	52	20	52	37
g	0	0	0	0	0	0	37	52	20	52	283	71	1	4	8	306	5	7	11	221	124	120
t	0	0	0	0	0	0	124	82	38	22	11	6	2	15	289	7	234	15	231	37	58	35
MA0106.3_shift0 (TP53) 
; positions_7nt_m3 versus MA0106.3 (TP53); m=1/4; ncol2=18; w=-6; offset=-6; strand=D; shift=0; score=0.470483; rACATGyCcgGrCATGTy----
; cor=; Ncor=
a	7544.0	10514.0	45.0	11931.0	1710.0	8.0	244.0	1228.0	1145.0	3851.0	3584.0	7104.0	0.0	12925.0	1825.0	327.0	879.0	1472.0	0	0	0	0
c	1037.0	116.0	19689.0	204.0	374.0	2.0	12014.0	17286.0	11875.0	1474.0	756.0	26.0	19350.0	250.0	118.0	33.0	3338.0	9183.0	0	0	0	0
g	6563.0	2433.0	13.0	653.0	137.0	20393.0	109.0	417.0	2151.0	9954.0	17846.0	8821.0	4.0	157.0	89.0	20549.0	116.0	825.0	0	0	0	0
t	2268.0	735.0	837.0	739.0	18893.0	0.0	7106.0	2642.0	3774.0	2118.0	1546.0	190.0	1.0	1155.0	17864.0	68.0	17859.0	9120.0	0	0	0	0
MA0861.2_shift11 (TP73) 
; positions_7nt_m3 versus MA0861.2 (TP73); m=2/4; ncol2=16; w=0; offset=5; strand=D; shift=11; score=0.464714; -----------rCATGTcyrrA
; cor=; Ncor=
a	0	0	0	0	0	0	0	0	0	0	0	6206.0	0.0	8760.0	3837.0	8.0	130.0	1377.0	2166.0	3488.0	3988.0	9639.0
c	0	0	0	0	0	0	0	0	0	0	0	429.0	10829.0	124.0	293.0	28.0	2591.0	8161.0	2940.0	2418.0	441.0	145.0
g	0	0	0	0	0	0	0	0	0	0	0	3304.0	0.0	557.0	806.0	11787.0	91.0	783.0	2230.0	3558.0	7797.0	1414.0
t	0	0	0	0	0	0	0	0	0	0	0	208.0	0.0	198.0	11480.0	1.0	11892.0	2749.0	4242.0	2457.0	1002.0	442.0
MA0525.2_shift0 (TP63) 
; positions_7nt_m3 versus MA0525.2 (TP63); m=3/4; ncol2=18; w=-6; offset=-6; strand=D; shift=0; score=0.419713; rACATGTygkrACATGTc----
; cor=; Ncor=
a	1586.0	2261.0	0.0	2246.0	692.0	0.0	14.0	97.0	649.0	112.0	993.0	2192.0	0.0	2151.0	75.0	0.0	49.0	701.0	0	0	0	0
c	26.0	1.0	2533.0	0.0	33.0	0.0	85.0	1025.0	478.0	681.0	1.0	0.0	2788.0	0.0	617.0	0.0	202.0	2099.0	0	0	0	0
g	997.0	185.0	0.0	76.0	0.0	4021.0	0.0	26.0	2070.0	1656.0	2132.0	48.0	0.0	1.0	8.0	3532.0	1.0	198.0	0	0	0	0
t	115.0	21.0	0.0	4.0	2353.0	0.0	3025.0	1961.0	13.0	829.0	47.0	45.0	0.0	192.0	2823.0	0.0	3126.0	606.0	0	0	0	0
MA2123.1_shift6 (Hand1) 
; positions_7nt_m3 versus MA2123.1 (Hand1); m=4/4; ncol2=9; w=0; offset=0; strand=D; shift=6; score=0.401487; ------tCCAGACCt-------
; cor=; Ncor=
a	0	0	0	0	0	0	177.0	84.0	8.0	1016.0	8.0	908.0	28.0	40.0	153.0	0	0	0	0	0	0	0
c	0	0	0	0	0	0	128.0	850.0	1036.0	16.0	24.0	33.0	955.0	962.0	235.0	0	0	0	0	0	0	0
g	0	0	0	0	0	0	148.0	101.0	12.0	10.0	1016.0	104.0	46.0	46.0	61.0	0	0	0	0	0	0	0
t	0	0	0	0	0	0	609.0	27.0	6.0	20.0	14.0	17.0	33.0	14.0	613.0	0	0	0	0	0	0	0