One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.024047_2026-04-21.024047_gRzMOf/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_nematodes_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/2026/04/21/peak-motifs.2026-04-21.024047_2026-04-21.024047_gRzMOf/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_JASPAR2024_CORE_nematodes_non-redundant

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; ywAAAAATwaw ; Alignment reference a 80 211 443 443 443 441 443 0 181 178 172 c 122 89 0 0 0 0 0 0 58 81 25 g 79 25 0 0 0 0 0 0 6 82 39 t 162 118 0 0 0 2 0 443 198 102 207

MA2184.1_shift2 (sox-3)
; positions_6nt_m1 versus MA2184.1 (sox-3); m=1/5; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.541973; --AAcAATTGw ; cor=; Ncor= a 0 0 82.0 82.0 0.0 89.0 100.0 10.0 4.0 0.0 26.0 c 0 0 4.0 9.0 65.0 5.0 0.0 0.0 14.0 13.0 15.0 g 0 0 4.0 4.0 11.0 5.0 0.0 0.0 0.0 77.0 0.0 t 0 0 9.0 4.0 23.0 0.0 0.0 89.0 81.0 9.0 58.0

MA2173.1_shift3 (mef-2)
; positions_6nt_m1 versus MA2173.1 (mef-2); m=2/5; ncol2=7; w=0; offset=3; strand=D; shift=3; score=0.541247; ---AAAATAG- ; cor=; Ncor= a 0 0 0 422.0 517.0 501.0 516.0 9.0 514.0 40.0 0 c 0 0 0 26.0 9.0 15.0 11.0 7.0 12.0 21.0 0 g 0 0 0 80.0 27.0 26.0 8.0 12.0 19.0 467.0 0 t 0 0 0 30.0 5.0 16.0 23.0 530.0 13.0 30.0 0

MA1440.1_shift2 (fkh-9)
; positions_6nt_m1 versus MA1440.1 (fkh-9); m=3/5; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.514735; --aAwAACAw- ; cor=; Ncor= a 0 0 527.0 809.0 655.0 983.0 999.0 47.0 968.0 574.0 0 c 0 0 236.0 16.0 93.0 15.0 0.0 780.0 0.0 75.0 0 g 0 0 236.0 0.0 0.0 0.0 0.0 0.0 0.0 75.0 0 t 0 0 0.0 174.0 250.0 0.0 0.0 171.0 31.0 274.0 0

MA2179.1_rc_shift3 (ceh-10_rc)
; positions_6nt_m1 versus MA2179.1_rc (ceh-10_rc); m=4/5; ncol2=11; w=0; offset=3; strand=R; shift=3; score=0.466061; ---AwAATTwd ; cor=; Ncor= a 0 0 0 75.0 47.0 85.0 91.0 8.0 0.0 64.0 25.0 c 0 0 0 0.0 0.0 0.0 0.0 0.0 8.0 0.0 7.0 g 0 0 0 8.0 0.0 7.0 8.0 0.0 0.0 0.0 39.0 t 0 0 0 16.0 52.0 7.0 0.0 91.0 91.0 35.0 28.0

MA1699.2_shift2 (ceh-38)
; positions_6nt_m1 versus MA1699.2 (ceh-38); m=5/5; ncol2=14; w=0; offset=2; strand=D; shift=2; score=0.457951; --AAAAATCrA ; cor=; Ncor= a 0 0 1760.0 2025.0 2060.0 2156.0 2135.0 11.0 11.0 1011.0 2150.0 c 0 0 34.0 16.0 34.0 4.0 8.0 17.0 2152.0 11.0 6.0 g 0 0 272.0 20.0 9.0 6.0 25.0 3.0 3.0 1133.0 13.0 t 0 0 111.0 116.0 74.0 11.0 9.0 2146.0 11.0 22.0 8.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; ywAAAAATwaw ; Alignment reference a 80 211 443 443 443 441 443 0 181 178 172 c 122 89 0 0 0 0 0 0 58 81 25 g 79 25 0 0 0 0 0 0 6 82 39 t 162 118 0 0 0 2 0 443 198 102 207
MA2184.1_shift2 (sox-3)				; positions_6nt_m1 versus MA2184.1 (sox-3); m=1/5; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.541973; --AAcAATTGw ; cor=; Ncor= a 0 0 82.0 82.0 0.0 89.0 100.0 10.0 4.0 0.0 26.0 c 0 0 4.0 9.0 65.0 5.0 0.0 0.0 14.0 13.0 15.0 g 0 0 4.0 4.0 11.0 5.0 0.0 0.0 0.0 77.0 0.0 t 0 0 9.0 4.0 23.0 0.0 0.0 89.0 81.0 9.0 58.0
MA2173.1_shift3 (mef-2)				; positions_6nt_m1 versus MA2173.1 (mef-2); m=2/5; ncol2=7; w=0; offset=3; strand=D; shift=3; score=0.541247; ---AAAATAG- ; cor=; Ncor= a 0 0 0 422.0 517.0 501.0 516.0 9.0 514.0 40.0 0 c 0 0 0 26.0 9.0 15.0 11.0 7.0 12.0 21.0 0 g 0 0 0 80.0 27.0 26.0 8.0 12.0 19.0 467.0 0 t 0 0 0 30.0 5.0 16.0 23.0 530.0 13.0 30.0 0
MA1440.1_shift2 (fkh-9)				; positions_6nt_m1 versus MA1440.1 (fkh-9); m=3/5; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.514735; --aAwAACAw- ; cor=; Ncor= a 0 0 527.0 809.0 655.0 983.0 999.0 47.0 968.0 574.0 0 c 0 0 236.0 16.0 93.0 15.0 0.0 780.0 0.0 75.0 0 g 0 0 236.0 0.0 0.0 0.0 0.0 0.0 0.0 75.0 0 t 0 0 0.0 174.0 250.0 0.0 0.0 171.0 31.0 274.0 0
MA2179.1_rc_shift3 (ceh-10_rc)				; positions_6nt_m1 versus MA2179.1_rc (ceh-10_rc); m=4/5; ncol2=11; w=0; offset=3; strand=R; shift=3; score=0.466061; ---AwAATTwd ; cor=; Ncor= a 0 0 0 75.0 47.0 85.0 91.0 8.0 0.0 64.0 25.0 c 0 0 0 0.0 0.0 0.0 0.0 0.0 8.0 0.0 7.0 g 0 0 0 8.0 0.0 7.0 8.0 0.0 0.0 0.0 39.0 t 0 0 0 16.0 52.0 7.0 0.0 91.0 91.0 35.0 28.0
MA1699.2_shift2 (ceh-38)				; positions_6nt_m1 versus MA1699.2 (ceh-38); m=5/5; ncol2=14; w=0; offset=2; strand=D; shift=2; score=0.457951; --AAAAATCrA ; cor=; Ncor= a 0 0 1760.0 2025.0 2060.0 2156.0 2135.0 11.0 11.0 1011.0 2150.0 c 0 0 34.0 16.0 34.0 4.0 8.0 17.0 2152.0 11.0 6.0 g 0 0 272.0 20.0 9.0 6.0 25.0 3.0 3.0 1133.0 13.0 t 0 0 111.0 116.0 74.0 11.0 9.0 2146.0 11.0 22.0 8.0