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.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1.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.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssGCCCGGCgsssg ; Alignment reference a 0 18 20 7 3 5 5 5 2 2 7 11 9 7 13 c 0 31 24 3 75 71 66 7 9 76 15 22 22 30 21 g 0 25 26 73 7 7 12 72 73 3 55 40 46 33 33 t 0 12 16 3 1 3 3 2 2 5 9 13 9 16 19

MA2328.1_shift0 (ZBED4)
; oligos_7nt_mkv2_m1 versus MA2328.1 (ZBED4); m=1/4; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.439789; CcCGCyCCGC----- ; cor=; Ncor= a 41.0 26.0 29.0 17.0 6.0 11.0 14.0 12.0 22.0 19.0 0 0 0 0 0 c 479.0 419.0 549.0 14.0 621.0 391.0 598.0 604.0 19.0 589.0 0 0 0 0 0 g 80.0 65.0 62.0 608.0 26.0 28.0 34.0 23.0 580.0 35.0 0 0 0 0 0 t 60.0 150.0 20.0 21.0 7.0 230.0 14.0 21.0 39.0 17.0 0 0 0 0 0

MA1513.2_rc_shift6 (KLF15_rc)
; oligos_7nt_mkv2_m1 versus MA1513.2_rc (KLF15_rc); m=2/4; ncol2=8; w=0; offset=5; strand=R; shift=6; score=0.433128; ------GGGCGGGg- ; cor=; Ncor= a 0 0 0 0 0 0 3.0 1.0 11.0 0.0 0.0 3.0 9.0 1809.0 0 c 0 0 0 0 0 0 100.0 359.0 2.0 11369.0 1.0 333.0 86.0 2117.0 0 g 0 0 0 0 0 0 11254.0 10954.0 11345.0 0.0 11368.0 10940.0 11234.0 6506.0 0 t 0 0 0 0 0 0 12.0 55.0 11.0 0.0 0.0 93.0 40.0 937.0 0

MA0471.3_shift7 (E2F6)
; oligos_7nt_mkv2_m1 versus MA0471.3 (E2F6); m=3/4; ncol2=8; w=0; offset=6; strand=D; shift=7; score=0.414802; -------GGCGGGAA ; cor=; Ncor= a 0 0 0 0 0 0 0 2110.0 266.0 3856.0 1173.0 338.0 354.0 29337.0 25725.0 c 0 0 0 0 0 0 0 1148.0 837.0 26424.0 539.0 434.0 834.0 1171.0 1595.0 g 0 0 0 0 0 0 0 29387.0 31790.0 693.0 30573.0 31973.0 31614.0 2322.0 5021.0 t 0 0 0 0 0 0 0 453.0 205.0 2125.0 813.0 353.0 296.0 268.0 757.0

MA1959.2_shift6 (KLF7)
; oligos_7nt_mkv2_m1 versus MA1959.2 (KLF7); m=4/4; ncol2=8; w=0; offset=5; strand=D; shift=6; score=0.403478; ------GGGCGKgG- ; cor=; Ncor= a 0 0 0 0 0 0 1.0 1.0 1.0 45.0 1.0 1.0 150.0 1.0 0 c 0 0 0 0 0 0 1.0 1.0 1.0 788.0 1.0 25.0 42.0 1.0 0 g 0 0 0 0 0 0 997.0 997.0 997.0 1.0 997.0 720.0 642.0 997.0 0 t 0 0 0 0 0 0 1.0 1.0 1.0 167.0 1.0 254.0 167.0 1.0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -ssGCCCGGCgsssg ; Alignment reference a 0 18 20 7 3 5 5 5 2 2 7 11 9 7 13 c 0 31 24 3 75 71 66 7 9 76 15 22 22 30 21 g 0 25 26 73 7 7 12 72 73 3 55 40 46 33 33 t 0 12 16 3 1 3 3 2 2 5 9 13 9 16 19
MA2328.1_shift0 (ZBED4)				; oligos_7nt_mkv2_m1 versus MA2328.1 (ZBED4); m=1/4; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score=0.439789; CcCGCyCCGC----- ; cor=; Ncor= a 41.0 26.0 29.0 17.0 6.0 11.0 14.0 12.0 22.0 19.0 0 0 0 0 0 c 479.0 419.0 549.0 14.0 621.0 391.0 598.0 604.0 19.0 589.0 0 0 0 0 0 g 80.0 65.0 62.0 608.0 26.0 28.0 34.0 23.0 580.0 35.0 0 0 0 0 0 t 60.0 150.0 20.0 21.0 7.0 230.0 14.0 21.0 39.0 17.0 0 0 0 0 0
MA1513.2_rc_shift6 (KLF15_rc)				; oligos_7nt_mkv2_m1 versus MA1513.2_rc (KLF15_rc); m=2/4; ncol2=8; w=0; offset=5; strand=R; shift=6; score=0.433128; ------GGGCGGGg- ; cor=; Ncor= a 0 0 0 0 0 0 3.0 1.0 11.0 0.0 0.0 3.0 9.0 1809.0 0 c 0 0 0 0 0 0 100.0 359.0 2.0 11369.0 1.0 333.0 86.0 2117.0 0 g 0 0 0 0 0 0 11254.0 10954.0 11345.0 0.0 11368.0 10940.0 11234.0 6506.0 0 t 0 0 0 0 0 0 12.0 55.0 11.0 0.0 0.0 93.0 40.0 937.0 0
MA0471.3_shift7 (E2F6)				; oligos_7nt_mkv2_m1 versus MA0471.3 (E2F6); m=3/4; ncol2=8; w=0; offset=6; strand=D; shift=7; score=0.414802; -------GGCGGGAA ; cor=; Ncor= a 0 0 0 0 0 0 0 2110.0 266.0 3856.0 1173.0 338.0 354.0 29337.0 25725.0 c 0 0 0 0 0 0 0 1148.0 837.0 26424.0 539.0 434.0 834.0 1171.0 1595.0 g 0 0 0 0 0 0 0 29387.0 31790.0 693.0 30573.0 31973.0 31614.0 2322.0 5021.0 t 0 0 0 0 0 0 0 453.0 205.0 2125.0 813.0 353.0 296.0 268.0 757.0
MA1959.2_shift6 (KLF7)				; oligos_7nt_mkv2_m1 versus MA1959.2 (KLF7); m=4/4; ncol2=8; w=0; offset=5; strand=D; shift=6; score=0.403478; ------GGGCGKgG- ; cor=; Ncor= a 0 0 0 0 0 0 1.0 1.0 1.0 45.0 1.0 1.0 150.0 1.0 0 c 0 0 0 0 0 0 1.0 1.0 1.0 788.0 1.0 25.0 42.0 1.0 0 g 0 0 0 0 0 0 997.0 997.0 997.0 1.0 997.0 720.0 642.0 997.0 0 t 0 0 0 0 0 0 1.0 1.0 1.0 167.0 1.0 254.0 167.0 1.0 0