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_m2/peak-motifs_oligos_7nt_mkv2_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/2025/05/16/peak-motifs.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; yaCACACACAca ; Alignment reference a 23 109 6 182 3 175 5 173 6 170 28 98 c 86 22 169 3 173 5 172 5 174 6 91 31 g 25 45 6 3 9 4 1 5 2 4 30 42 t 56 14 9 2 5 6 12 7 8 10 41 19

MA1107.3_shift0 (KLF9)
; oligos_7nt_mkv2_m2 versus MA1107.3 (KLF9); m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.687284; gCCACACCCAC- ; cor=; Ncor= a 2862.0 4664.0 287.0 21899.0 221.0 19187.0 224.0 2428.0 146.0 18837.0 792.0 0 c 4342.0 17839.0 24709.0 2559.0 24863.0 1070.0 24365.0 22117.0 24682.0 4339.0 20644.0 0 g 16852.0 1660.0 291.0 708.0 353.0 4340.0 735.0 605.0 205.0 852.0 1778.0 0 t 1523.0 1416.0 292.0 413.0 142.0 982.0 255.0 429.0 546.0 1551.0 2365.0 0

MA1155.1_shift0 (ZSCAN4)
; oligos_7nt_mkv2_m2 versus MA1155.1 (ZSCAN4); m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.567915; tGCACACmCTGa ; cor=; Ncor= a 257.0 290.0 0.0 1292.0 0.0 1281.0 3.0 772.0 7.0 8.0 3.0 1118.0 c 383.0 2.0 1676.0 0.0 1665.0 0.0 1702.0 374.0 1684.0 11.0 50.0 107.0 g 112.0 1737.0 1.0 0.0 0.0 2.0 0.0 320.0 0.0 75.0 1873.0 230.0 t 1373.0 0.0 0.0 2.0 0.0 2.0 73.0 8.0 2.0 1699.0 218.0 362.0

MA1523.2_shift2 (MSANTD3)
; oligos_7nt_mkv2_m2 versus MA1523.2 (MSANTD3); m=3/3; ncol2=7; w=0; offset=2; strand=D; shift=2; score=0.436949; --CACTCAm--- ; cor=; Ncor= a 0 0 64.0 980.0 31.0 37.0 47.0 775.0 271.0 0 0 0 c 0 0 723.0 0.0 896.0 7.0 862.0 140.0 568.0 0 0 0 g 0 0 31.0 2.0 27.0 0.0 29.0 24.0 63.0 0 0 0 t 0 0 180.0 16.0 45.0 954.0 60.0 59.0 96.0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; yaCACACACAca ; Alignment reference a 23 109 6 182 3 175 5 173 6 170 28 98 c 86 22 169 3 173 5 172 5 174 6 91 31 g 25 45 6 3 9 4 1 5 2 4 30 42 t 56 14 9 2 5 6 12 7 8 10 41 19
MA1107.3_shift0 (KLF9)				; oligos_7nt_mkv2_m2 versus MA1107.3 (KLF9); m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.687284; gCCACACCCAC- ; cor=; Ncor= a 2862.0 4664.0 287.0 21899.0 221.0 19187.0 224.0 2428.0 146.0 18837.0 792.0 0 c 4342.0 17839.0 24709.0 2559.0 24863.0 1070.0 24365.0 22117.0 24682.0 4339.0 20644.0 0 g 16852.0 1660.0 291.0 708.0 353.0 4340.0 735.0 605.0 205.0 852.0 1778.0 0 t 1523.0 1416.0 292.0 413.0 142.0 982.0 255.0 429.0 546.0 1551.0 2365.0 0
MA1155.1_shift0 (ZSCAN4)				; oligos_7nt_mkv2_m2 versus MA1155.1 (ZSCAN4); m=2/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.567915; tGCACACmCTGa ; cor=; Ncor= a 257.0 290.0 0.0 1292.0 0.0 1281.0 3.0 772.0 7.0 8.0 3.0 1118.0 c 383.0 2.0 1676.0 0.0 1665.0 0.0 1702.0 374.0 1684.0 11.0 50.0 107.0 g 112.0 1737.0 1.0 0.0 0.0 2.0 0.0 320.0 0.0 75.0 1873.0 230.0 t 1373.0 0.0 0.0 2.0 0.0 2.0 73.0 8.0 2.0 1699.0 218.0 362.0
MA1523.2_shift2 (MSANTD3)				; oligos_7nt_mkv2_m2 versus MA1523.2 (MSANTD3); m=3/3; ncol2=7; w=0; offset=2; strand=D; shift=2; score=0.436949; --CACTCAm--- ; cor=; Ncor= a 0 0 64.0 980.0 31.0 37.0 47.0 775.0 271.0 0 0 0 c 0 0 723.0 0.0 896.0 7.0 862.0 140.0 568.0 0 0 0 g 0 0 31.0 2.0 27.0 0.0 29.0 24.0 63.0 0 0 0 t 0 0 180.0 16.0 45.0 954.0 60.0 59.0 96.0 0 0 0