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.2025-05-16.184256_2025-05-16.184256_DOHBqC/results/discovered_motifs/oligos_6nt_mkv1_m4/peak-motifs_oligos_6nt_mkv1_m4.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.2025-05-16.184256_2025-05-16.184256_DOHBqC/results/discovered_motifs/oligos_6nt_mkv1_m4/peak-motifs_oligos_6nt_mkv1_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m4_shift2 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=2; ncol=12; --dgCAGAGAgw ; Alignment reference a 0 0 4 2 0 10 0 10 0 10 1 4 c 0 0 0 2 10 0 0 0 0 0 2 1 g 0 0 3 5 0 0 10 0 10 0 6 2 t 0 0 3 1 0 0 0 0 0 0 1 3

MA1731.2_rc_shift4 (ZNF768_rc)
; oligos_6nt_mkv1_m4 versus MA1731.2_rc (ZNF768_rc); m=1/4; ncol2=9; w=0; offset=2; strand=R; shift=4; score=0.689009; ----CAGAGAgG ; cor=; Ncor= a 0 0 0 0 1.0 987.0 1.0 945.0 20.0 917.0 123.0 141.0 c 0 0 0 0 973.0 11.0 11.0 43.0 29.0 11.0 179.0 62.0 g 0 0 0 0 25.0 1.0 987.0 6.0 950.0 39.0 655.0 768.0 t 0 0 0 0 1.0 1.0 1.0 6.0 1.0 34.0 43.0 29.0

MA1593.2_shift0 (ZNF317)
; oligos_6nt_mkv1_m4 versus MA1593.2 (ZNF317); m=2/4; ncol2=8; w=-2; offset=-2; strand=D; shift=0; score=0.449161; ACAGCAGA---- ; cor=; Ncor= a 9381.0 281.0 10344.0 691.0 395.0 9323.0 284.0 10825.0 0 0 0 0 c 357.0 10821.0 85.0 192.0 10608.0 250.0 186.0 208.0 0 0 0 0 g 480.0 183.0 317.0 10374.0 223.0 289.0 10730.0 206.0 0 0 0 0 t 1245.0 178.0 717.0 206.0 237.0 1601.0 263.0 224.0 0 0 0 0

MA0508.4_rc_shift6 (PRDM1_rc)
; oligos_6nt_mkv1_m4 versus MA0508.4_rc (PRDM1_rc); m=3/4; ncol2=7; w=0; offset=4; strand=R; shift=6; score=0.430944; ------GAGAAA ; cor=; Ncor= a 0 0 0 0 0 0 660.0 49466.0 432.0 52619.0 50943.0 52905.0 c 0 0 0 0 0 0 290.0 1390.0 207.0 561.0 1011.0 826.0 g 0 0 0 0 0 0 52821.0 1076.0 53465.0 488.0 1346.0 467.0 t 0 0 0 0 0 0 1710.0 3549.0 1377.0 1813.0 2181.0 1283.0

MA0092.2_rc_shift0 (Hand1::Tcf3_rc)
; oligos_6nt_mkv1_m4 versus MA0092.2_rc (Hand1::Tcf3_rc); m=4/4; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.411895; awkCCAGAy--- ; cor=; Ncor= a 16.0 10.0 5.0 1.0 0.0 29.0 1.0 24.0 4.0 0 0 0 c 4.0 3.0 1.0 25.0 29.0 0.0 0.0 1.0 15.0 0 0 0 g 4.0 0.0 14.0 3.0 0.0 0.0 28.0 2.0 0.0 0 0 0 t 5.0 16.0 9.0 0.0 0.0 0.0 0.0 2.0 10.0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m4_shift2 (oligos_6nt_mkv1_m4)				; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=2; ncol=12; --dgCAGAGAgw ; Alignment reference a 0 0 4 2 0 10 0 10 0 10 1 4 c 0 0 0 2 10 0 0 0 0 0 2 1 g 0 0 3 5 0 0 10 0 10 0 6 2 t 0 0 3 1 0 0 0 0 0 0 1 3
MA1731.2_rc_shift4 (ZNF768_rc)				; oligos_6nt_mkv1_m4 versus MA1731.2_rc (ZNF768_rc); m=1/4; ncol2=9; w=0; offset=2; strand=R; shift=4; score=0.689009; ----CAGAGAgG ; cor=; Ncor= a 0 0 0 0 1.0 987.0 1.0 945.0 20.0 917.0 123.0 141.0 c 0 0 0 0 973.0 11.0 11.0 43.0 29.0 11.0 179.0 62.0 g 0 0 0 0 25.0 1.0 987.0 6.0 950.0 39.0 655.0 768.0 t 0 0 0 0 1.0 1.0 1.0 6.0 1.0 34.0 43.0 29.0
MA1593.2_shift0 (ZNF317)				; oligos_6nt_mkv1_m4 versus MA1593.2 (ZNF317); m=2/4; ncol2=8; w=-2; offset=-2; strand=D; shift=0; score=0.449161; ACAGCAGA---- ; cor=; Ncor= a 9381.0 281.0 10344.0 691.0 395.0 9323.0 284.0 10825.0 0 0 0 0 c 357.0 10821.0 85.0 192.0 10608.0 250.0 186.0 208.0 0 0 0 0 g 480.0 183.0 317.0 10374.0 223.0 289.0 10730.0 206.0 0 0 0 0 t 1245.0 178.0 717.0 206.0 237.0 1601.0 263.0 224.0 0 0 0 0
MA0508.4_rc_shift6 (PRDM1_rc)				; oligos_6nt_mkv1_m4 versus MA0508.4_rc (PRDM1_rc); m=3/4; ncol2=7; w=0; offset=4; strand=R; shift=6; score=0.430944; ------GAGAAA ; cor=; Ncor= a 0 0 0 0 0 0 660.0 49466.0 432.0 52619.0 50943.0 52905.0 c 0 0 0 0 0 0 290.0 1390.0 207.0 561.0 1011.0 826.0 g 0 0 0 0 0 0 52821.0 1076.0 53465.0 488.0 1346.0 467.0 t 0 0 0 0 0 0 1710.0 3549.0 1377.0 1813.0 2181.0 1283.0
MA0092.2_rc_shift0 (Hand1::Tcf3_rc)				; oligos_6nt_mkv1_m4 versus MA0092.2_rc (Hand1::Tcf3_rc); m=4/4; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.411895; awkCCAGAy--- ; cor=; Ncor= a 16.0 10.0 5.0 1.0 0.0 29.0 1.0 24.0 4.0 0 0 0 c 4.0 3.0 1.0 25.0 29.0 0.0 0.0 1.0 15.0 0 0 0 g 4.0 0.0 14.0 3.0 0.0 0.0 28.0 2.0 0.0 0 0 0 t 5.0 16.0 9.0 0.0 0.0 0.0 0.0 2.0 10.0 0 0 0