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_m2/peak-motifs_positions_7nt_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/2025/11/25/peak-motifs.2025-11-25.143236_2025-11-25.143236_C5OFib/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift2 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --AaAAAAAAAaA ; Alignment reference a 0 0 19250 18525 26699 26379 26277 25271 26112 26259 26647 18371 19321 c 0 0 2006 1667 22 44 57 77 32 58 365 2091 2333 g 0 0 2115 1773 85 61 56 54 32 38 17 1868 2269 t 0 0 3902 5308 467 789 883 1871 1097 918 244 4943 3350

MA1125.2_shift5 (ZNF384)
; positions_7nt_m2 versus MA1125.2 (ZNF384); m=1/4; ncol2=8; w=0; offset=3; strand=D; shift=5; score=0.725447; -----AAAAAAaa ; cor=; Ncor= a 0 0 0 0 0 30354.0 30191.0 30072.0 30252.0 30202.0 30406.0 20322.0 18916.0 c 0 0 0 0 0 7.0 35.0 21.0 13.0 26.0 6.0 2908.0 3963.0 g 0 0 0 0 0 13.0 19.0 26.0 15.0 14.0 0.0 2767.0 2898.0 t 0 0 0 0 0 59.0 188.0 314.0 153.0 191.0 21.0 4436.0 4656.0

MA1487.3_shift0 (FOXE1)
; positions_7nt_m2 versus MA1487.3 (FOXE1); m=2/4; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.538882; yTAARyAAACAa- ; cor=; Ncor= a 86.0 581.0 3126.0 2547.0 2255.0 587.0 3126.0 3126.0 3126.0 0.0 3126.0 2026.0 0 c 1646.0 43.0 28.0 113.0 117.0 1062.0 362.0 90.0 0.0 3126.0 32.0 392.0 0 g 57.0 0.0 402.0 116.0 871.0 17.0 0.0 0.0 23.0 0.0 18.0 258.0 0 t 1479.0 2545.0 43.0 579.0 27.0 2064.0 20.0 53.0 9.0 85.0 110.0 450.0 0

MA2124.1_rc_shift6 (Hmga1_rc)
; positions_7nt_m2 versus MA2124.1_rc (Hmga1_rc); m=3/4; ncol2=8; w=0; offset=4; strand=R; shift=6; score=0.422334; ------wTAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 11340.0 542.0 24333.0 24654.0 24779.0 24269.0 24172.0 c 0 0 0 0 0 0 2438.0 358.0 294.0 237.0 138.0 303.0 421.0 g 0 0 0 0 0 0 2348.0 473.0 409.0 264.0 194.0 200.0 393.0 t 0 0 0 0 0 0 9680.0 24433.0 770.0 651.0 695.0 1034.0 820.0

MA0901.3_shift0 (HOXB13)
; positions_7nt_m2 versus MA0901.3 (HOXB13); m=4/4; ncol2=9; w=-2; offset=-2; strand=D; shift=0; score=0.407978; cCAATAAAA---- ; cor=; Ncor= a 11896.0 4212.0 66409.0 73044.0 421.0 73612.0 75997.0 76077.0 70230.0 0 0 0 0 c 47674.0 65312.0 4611.0 726.0 550.0 523.0 599.0 760.0 2465.0 0 0 0 0 g 9096.0 582.0 351.0 1913.0 586.0 1083.0 490.0 625.0 1882.0 0 0 0 0 t 10048.0 8608.0 7343.0 3031.0 77157.0 3496.0 1628.0 1252.0 4137.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift2 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --AaAAAAAAAaA ; Alignment reference a 0 0 19250 18525 26699 26379 26277 25271 26112 26259 26647 18371 19321 c 0 0 2006 1667 22 44 57 77 32 58 365 2091 2333 g 0 0 2115 1773 85 61 56 54 32 38 17 1868 2269 t 0 0 3902 5308 467 789 883 1871 1097 918 244 4943 3350
MA1125.2_shift5 (ZNF384)				; positions_7nt_m2 versus MA1125.2 (ZNF384); m=1/4; ncol2=8; w=0; offset=3; strand=D; shift=5; score=0.725447; -----AAAAAAaa ; cor=; Ncor= a 0 0 0 0 0 30354.0 30191.0 30072.0 30252.0 30202.0 30406.0 20322.0 18916.0 c 0 0 0 0 0 7.0 35.0 21.0 13.0 26.0 6.0 2908.0 3963.0 g 0 0 0 0 0 13.0 19.0 26.0 15.0 14.0 0.0 2767.0 2898.0 t 0 0 0 0 0 59.0 188.0 314.0 153.0 191.0 21.0 4436.0 4656.0
MA1487.3_shift0 (FOXE1)				; positions_7nt_m2 versus MA1487.3 (FOXE1); m=2/4; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.538882; yTAARyAAACAa- ; cor=; Ncor= a 86.0 581.0 3126.0 2547.0 2255.0 587.0 3126.0 3126.0 3126.0 0.0 3126.0 2026.0 0 c 1646.0 43.0 28.0 113.0 117.0 1062.0 362.0 90.0 0.0 3126.0 32.0 392.0 0 g 57.0 0.0 402.0 116.0 871.0 17.0 0.0 0.0 23.0 0.0 18.0 258.0 0 t 1479.0 2545.0 43.0 579.0 27.0 2064.0 20.0 53.0 9.0 85.0 110.0 450.0 0
MA2124.1_rc_shift6 (Hmga1_rc)				; positions_7nt_m2 versus MA2124.1_rc (Hmga1_rc); m=3/4; ncol2=8; w=0; offset=4; strand=R; shift=6; score=0.422334; ------wTAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 11340.0 542.0 24333.0 24654.0 24779.0 24269.0 24172.0 c 0 0 0 0 0 0 2438.0 358.0 294.0 237.0 138.0 303.0 421.0 g 0 0 0 0 0 0 2348.0 473.0 409.0 264.0 194.0 200.0 393.0 t 0 0 0 0 0 0 9680.0 24433.0 770.0 651.0 695.0 1034.0 820.0
MA0901.3_shift0 (HOXB13)				; positions_7nt_m2 versus MA0901.3 (HOXB13); m=4/4; ncol2=9; w=-2; offset=-2; strand=D; shift=0; score=0.407978; cCAATAAAA---- ; cor=; Ncor= a 11896.0 4212.0 66409.0 73044.0 421.0 73612.0 75997.0 76077.0 70230.0 0 0 0 0 c 47674.0 65312.0 4611.0 726.0 550.0 523.0 599.0 760.0 2465.0 0 0 0 0 g 9096.0 582.0 351.0 1913.0 586.0 1083.0 490.0 625.0 1882.0 0 0 0 0 t 10048.0 8608.0 7343.0 3031.0 77157.0 3496.0 1628.0 1252.0 4137.0 0 0 0 0