One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m2/peak-motifs_oligos_8nt_mkv1_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_plants_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/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m2/peak-motifs_oligos_8nt_mkv1_m2_vs_db_JASPAR2024_CORE_plants_non-redundant

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2)
; oligos_8nt_mkv1_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; GhGAAGTGCAww ; Alignment reference a 0 1 0 3 3 0 0 0 0 3 2 2 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 1

MA2419.1_shift2 (UB3)
; oligos_8nt_mkv1_m2 versus MA2419.1 (UB3); m=1/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.630406; --gAAGTACAAc ; cor=; Ncor= a 0 0 3823.0 17244.0 18109.0 293.0 754.0 18975.0 322.0 16933.0 16719.0 4243.0 c 0 0 2963.0 566.0 527.0 269.0 287.0 196.0 18929.0 795.0 1201.0 11116.0 g 0 0 11905.0 1023.0 855.0 18318.0 1213.0 675.0 693.0 1162.0 629.0 3465.0 t 0 0 1439.0 1297.0 639.0 1250.0 17876.0 284.0 186.0 1240.0 1581.0 1306.0

MA2420.1_shift3 (SBP6)
; oligos_8nt_mkv1_m2 versus MA2420.1 (SBP6); m=2/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.529629; ---AAGTACAA- ; cor=; Ncor= a 0 0 0 11102.0 11189.0 127.0 121.0 12984.0 132.0 12012.0 10537.0 0 c 0 0 0 376.0 290.0 62.0 55.0 51.0 12922.0 339.0 891.0 0 g 0 0 0 1080.0 1425.0 12390.0 479.0 66.0 42.0 330.0 490.0 0 t 0 0 0 607.0 261.0 586.0 12510.0 64.0 69.0 484.0 1247.0 0

MA2421.1_shift3 (SBP8)
; oligos_8nt_mkv1_m2 versus MA2421.1 (SBP8); m=3/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.499596; ---arGTACAa- ; cor=; Ncor= a 0 0 0 28920.0 30785.0 200.0 256.0 48160.0 275.0 46945.0 27864.0 0 c 0 0 0 3935.0 226.0 70.0 231.0 67.0 47947.0 397.0 5026.0 0 g 0 0 0 6297.0 17080.0 48049.0 509.0 52.0 79.0 519.0 5397.0 0 t 0 0 0 9248.0 309.0 81.0 47404.0 121.0 99.0 539.0 10113.0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2)				; oligos_8nt_mkv1_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; GhGAAGTGCAww ; Alignment reference a 0 1 0 3 3 0 0 0 0 3 2 2 c 0 1 0 0 0 0 0 0 3 0 0 0 g 3 0 3 0 0 3 0 3 0 0 0 0 t 0 1 0 0 0 0 3 0 0 0 1 1
MA2419.1_shift2 (UB3)				; oligos_8nt_mkv1_m2 versus MA2419.1 (UB3); m=1/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.630406; --gAAGTACAAc ; cor=; Ncor= a 0 0 3823.0 17244.0 18109.0 293.0 754.0 18975.0 322.0 16933.0 16719.0 4243.0 c 0 0 2963.0 566.0 527.0 269.0 287.0 196.0 18929.0 795.0 1201.0 11116.0 g 0 0 11905.0 1023.0 855.0 18318.0 1213.0 675.0 693.0 1162.0 629.0 3465.0 t 0 0 1439.0 1297.0 639.0 1250.0 17876.0 284.0 186.0 1240.0 1581.0 1306.0
MA2420.1_shift3 (SBP6)				; oligos_8nt_mkv1_m2 versus MA2420.1 (SBP6); m=2/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.529629; ---AAGTACAA- ; cor=; Ncor= a 0 0 0 11102.0 11189.0 127.0 121.0 12984.0 132.0 12012.0 10537.0 0 c 0 0 0 376.0 290.0 62.0 55.0 51.0 12922.0 339.0 891.0 0 g 0 0 0 1080.0 1425.0 12390.0 479.0 66.0 42.0 330.0 490.0 0 t 0 0 0 607.0 261.0 586.0 12510.0 64.0 69.0 484.0 1247.0 0
MA2421.1_shift3 (SBP8)				; oligos_8nt_mkv1_m2 versus MA2421.1 (SBP8); m=3/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.499596; ---arGTACAa- ; cor=; Ncor= a 0 0 0 28920.0 30785.0 200.0 256.0 48160.0 275.0 46945.0 27864.0 0 c 0 0 0 3935.0 226.0 70.0 231.0 67.0 47947.0 397.0 5026.0 0 g 0 0 0 6297.0 17080.0 48049.0 509.0 52.0 79.0 519.0 5397.0 0 t 0 0 0 9248.0 309.0 81.0 47404.0 121.0 99.0 539.0 10113.0 0