One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/04/peak-motifs.2026-01-04.175405_2026-01-04.175405_YulKOI/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_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/2026/01/04/peak-motifs.2026-01-04.175405_2026-01-04.175405_YulKOI/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wwACTAAGAww ; Alignment reference a 0 2343 2054 7053 522 264 6759 6637 600 6842 2551 2461 c 0 1135 1108 161 6557 179 300 92 304 262 1318 1507 g 0 1471 1388 135 308 153 243 231 6137 175 1319 1224 t 0 2777 3176 377 339 7130 424 766 685 447 2538 2534

MA1963.2_shift4 (SATB1)
; oligos_6nt_test_vs_ctrl_m3 versus MA1963.2 (SATB1); m=1/3; ncol2=7; w=0; offset=3; strand=D; shift=4; score=0.488437; ----CTAATAA- ; cor=; Ncor= a 0 0 0 0 262.0 492.0 33670.0 32708.0 288.0 32009.0 30660.0 0 c 0 0 0 0 33122.0 195.0 164.0 115.0 128.0 485.0 881.0 0 g 0 0 0 0 140.0 37.0 221.0 120.0 123.0 889.0 1071.0 0 t 0 0 0 0 700.0 33500.0 169.0 1281.0 33685.0 841.0 1612.0 0

MA0895.2_rc_shift0 (HMBOX1_rc)
; oligos_6nt_test_vs_ctrl_m3 versus MA0895.2_rc (HMBOX1_rc); m=2/3; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score=0.425873; kTAACTA----- ; cor=; Ncor= a 140.0 102.0 1231.0 1231.0 5.0 44.0 1231.0 0 0 0 0 0 c 130.0 17.0 8.0 5.0 1231.0 367.0 63.0 0 0 0 0 0 g 478.0 4.0 50.0 1.0 51.0 0.0 25.0 0 0 0 0 0 t 753.0 1231.0 237.0 26.0 2.0 1231.0 75.0 0 0 0 0 0

MA0442.3_shift3 (SOX10)
; oligos_6nt_test_vs_ctrl_m3 versus MA0442.3 (SOX10); m=3/3; ncol2=6; w=0; offset=2; strand=D; shift=3; score=0.411112; ---ACAAAG--- ; cor=; Ncor= a 0 0 0 2023.0 3.0 2029.0 1968.0 1959.0 10.0 0 0 0 c 0 0 0 4.0 1989.0 7.0 28.0 23.0 13.0 0 0 0 g 0 0 0 3.0 11.0 7.0 20.0 12.0 2012.0 0 0 0 t 0 0 0 25.0 52.0 12.0 39.0 61.0 20.0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wwACTAAGAww ; Alignment reference a 0 2343 2054 7053 522 264 6759 6637 600 6842 2551 2461 c 0 1135 1108 161 6557 179 300 92 304 262 1318 1507 g 0 1471 1388 135 308 153 243 231 6137 175 1319 1224 t 0 2777 3176 377 339 7130 424 766 685 447 2538 2534
MA1963.2_shift4 (SATB1)				; oligos_6nt_test_vs_ctrl_m3 versus MA1963.2 (SATB1); m=1/3; ncol2=7; w=0; offset=3; strand=D; shift=4; score=0.488437; ----CTAATAA- ; cor=; Ncor= a 0 0 0 0 262.0 492.0 33670.0 32708.0 288.0 32009.0 30660.0 0 c 0 0 0 0 33122.0 195.0 164.0 115.0 128.0 485.0 881.0 0 g 0 0 0 0 140.0 37.0 221.0 120.0 123.0 889.0 1071.0 0 t 0 0 0 0 700.0 33500.0 169.0 1281.0 33685.0 841.0 1612.0 0
MA0895.2_rc_shift0 (HMBOX1_rc)				; oligos_6nt_test_vs_ctrl_m3 versus MA0895.2_rc (HMBOX1_rc); m=2/3; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score=0.425873; kTAACTA----- ; cor=; Ncor= a 140.0 102.0 1231.0 1231.0 5.0 44.0 1231.0 0 0 0 0 0 c 130.0 17.0 8.0 5.0 1231.0 367.0 63.0 0 0 0 0 0 g 478.0 4.0 50.0 1.0 51.0 0.0 25.0 0 0 0 0 0 t 753.0 1231.0 237.0 26.0 2.0 1231.0 75.0 0 0 0 0 0
MA0442.3_shift3 (SOX10)				; oligos_6nt_test_vs_ctrl_m3 versus MA0442.3 (SOX10); m=3/3; ncol2=6; w=0; offset=2; strand=D; shift=3; score=0.411112; ---ACAAAG--- ; cor=; Ncor= a 0 0 0 2023.0 3.0 2029.0 1968.0 1959.0 10.0 0 0 0 c 0 0 0 4.0 1989.0 7.0 28.0 23.0 13.0 0 0 0 g 0 0 0 3.0 11.0 7.0 20.0 12.0 2012.0 0 0 0 t 0 0 0 25.0 52.0 12.0 39.0 61.0 20.0 0 0 0