One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/25/peak-motifs.2025-11-25.143236_2025-11-25.143236_C5OFib/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_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/2025/11/25/peak-motifs.2025-11-25.143236_2025-11-25.143236_C5OFib/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m4_shift1 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=13; shift=1; ncol=14; -caCAaAGACACam ; Alignment reference a 0 624 1332 99 2673 1955 2617 162 2531 140 2594 139 1103 762 c 0 1152 418 2632 51 610 98 445 184 2642 116 2563 629 901 g 0 534 635 98 100 209 125 2129 116 55 116 124 640 655 t 0 617 542 98 103 153 87 191 96 90 101 101 555 609

MA0867.3_shift1 (SOX4)
; positions_7nt_m4 versus MA0867.3 (SOX4); m=1/4; ncol2=8; w=0; offset=0; strand=D; shift=1; score=0.480619; -aACAAwGr----- ; cor=; Ncor= a 0 5582.0 5582.0 0.0 5582.0 5582.0 5582.0 1018.0 2093.0 0 0 0 0 0 c 0 951.0 0.0 5582.0 1.0 6.0 120.0 64.0 1422.0 0 0 0 0 0 g 0 2047.0 0.0 37.0 6.0 11.0 50.0 5582.0 3489.0 0 0 0 0 0 t 0 431.0 9.0 33.0 0.0 0.0 2719.0 83.0 174.0 0 0 0 0 0

MA0769.3_rc_shift1 (TCF7_rc)
; positions_7nt_m4 versus MA0769.3_rc (TCF7_rc); m=2/4; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.446663; -wTCAAAG------ ; cor=; Ncor= a 0 8498.0 239.0 478.0 14489.0 14178.0 14556.0 157.0 0 0 0 0 0 0 c 0 1220.0 115.0 13972.0 83.0 266.0 67.0 206.0 0 0 0 0 0 0 g 0 855.0 63.0 278.0 62.0 248.0 125.0 14379.0 0 0 0 0 0 0 t 0 4421.0 14577.0 266.0 360.0 302.0 246.0 252.0 0 0 0 0 0 0

MA0869.3_shift0 (Sox11)
; positions_7nt_m4 versus MA0869.3 (Sox11); m=3/4; ncol2=8; w=-1; offset=-1; strand=D; shift=0; score=0.442784; GAACAAAG------ ; cor=; Ncor= a 1014.0 7912.0 9856.0 119.0 10020.0 9676.0 9276.0 506.0 0 0 0 0 0 0 c 764.0 766.0 100.0 9471.0 108.0 264.0 61.0 148.0 0 0 0 0 0 0 g 8063.0 1298.0 211.0 501.0 49.0 248.0 233.0 9486.0 0 0 0 0 0 0 t 407.0 272.0 81.0 157.0 71.0 60.0 678.0 108.0 0 0 0 0 0 0

MA0442.3_shift2 (SOX10)
; positions_7nt_m4 versus MA0442.3 (SOX10); m=4/4; ncol2=6; w=0; offset=1; strand=D; shift=2; score=0.436043; --ACAAAG------ ; cor=; Ncor= a 0 0 2023.0 3.0 2029.0 1968.0 1959.0 10.0 0 0 0 0 0 0 c 0 0 4.0 1989.0 7.0 28.0 23.0 13.0 0 0 0 0 0 0 g 0 0 3.0 11.0 7.0 20.0 12.0 2012.0 0 0 0 0 0 0 t 0 0 25.0 52.0 12.0 39.0 61.0 20.0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m4_shift1 (positions_7nt_m4)				; positions_7nt_m4; m=0 (reference); ncol1=13; shift=1; ncol=14; -caCAaAGACACam ; Alignment reference a 0 624 1332 99 2673 1955 2617 162 2531 140 2594 139 1103 762 c 0 1152 418 2632 51 610 98 445 184 2642 116 2563 629 901 g 0 534 635 98 100 209 125 2129 116 55 116 124 640 655 t 0 617 542 98 103 153 87 191 96 90 101 101 555 609
MA0867.3_shift1 (SOX4)				; positions_7nt_m4 versus MA0867.3 (SOX4); m=1/4; ncol2=8; w=0; offset=0; strand=D; shift=1; score=0.480619; -aACAAwGr----- ; cor=; Ncor= a 0 5582.0 5582.0 0.0 5582.0 5582.0 5582.0 1018.0 2093.0 0 0 0 0 0 c 0 951.0 0.0 5582.0 1.0 6.0 120.0 64.0 1422.0 0 0 0 0 0 g 0 2047.0 0.0 37.0 6.0 11.0 50.0 5582.0 3489.0 0 0 0 0 0 t 0 431.0 9.0 33.0 0.0 0.0 2719.0 83.0 174.0 0 0 0 0 0
MA0769.3_rc_shift1 (TCF7_rc)				; positions_7nt_m4 versus MA0769.3_rc (TCF7_rc); m=2/4; ncol2=7; w=0; offset=0; strand=R; shift=1; score=0.446663; -wTCAAAG------ ; cor=; Ncor= a 0 8498.0 239.0 478.0 14489.0 14178.0 14556.0 157.0 0 0 0 0 0 0 c 0 1220.0 115.0 13972.0 83.0 266.0 67.0 206.0 0 0 0 0 0 0 g 0 855.0 63.0 278.0 62.0 248.0 125.0 14379.0 0 0 0 0 0 0 t 0 4421.0 14577.0 266.0 360.0 302.0 246.0 252.0 0 0 0 0 0 0
MA0869.3_shift0 (Sox11)				; positions_7nt_m4 versus MA0869.3 (Sox11); m=3/4; ncol2=8; w=-1; offset=-1; strand=D; shift=0; score=0.442784; GAACAAAG------ ; cor=; Ncor= a 1014.0 7912.0 9856.0 119.0 10020.0 9676.0 9276.0 506.0 0 0 0 0 0 0 c 764.0 766.0 100.0 9471.0 108.0 264.0 61.0 148.0 0 0 0 0 0 0 g 8063.0 1298.0 211.0 501.0 49.0 248.0 233.0 9486.0 0 0 0 0 0 0 t 407.0 272.0 81.0 157.0 71.0 60.0 678.0 108.0 0 0 0 0 0 0
MA0442.3_shift2 (SOX10)				; positions_7nt_m4 versus MA0442.3 (SOX10); m=4/4; ncol2=6; w=0; offset=1; strand=D; shift=2; score=0.436043; --ACAAAG------ ; cor=; Ncor= a 0 0 2023.0 3.0 2029.0 1968.0 1959.0 10.0 0 0 0 0 0 0 c 0 0 4.0 1989.0 7.0 28.0 23.0 13.0 0 0 0 0 0 0 g 0 0 3.0 11.0 7.0 20.0 12.0 2012.0 0 0 0 0 0 0 t 0 0 25.0 52.0 12.0 39.0 61.0 20.0 0 0 0 0 0 0