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.2026-04-21.015247_2026-04-21.015247_DTyOML/results/discovered_motifs/peak-motifs_motifs_discovered.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.2026-04-21.015247_2026-04-21.015247_DTyOML/results/discovered_vs_db/peak-motifs_motifs_vs_db_JASPAR2024_CORE_nematodes_non-redundant.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; twAAAAAAww ; Alignment reference a 115 130 507 507 507 507 507 507 130 182 c 104 118 0 0 0 0 0 0 60 108 g 119 105 0 0 0 0 0 0 56 46 t 169 154 0 0 0 0 0 0 261 171
MA1440.1_shift1 (fkh-9)				; positions_6nt_m2 versus MA1440.1 (fkh-9); m=1/2; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.595686; -aAwAACAw- ; cor=; Ncor= a 0 527.0 809.0 655.0 983.0 999.0 47.0 968.0 574.0 0 c 0 236.0 16.0 93.0 15.0 0.0 780.0 0.0 75.0 0 g 0 236.0 0.0 0.0 0.0 0.0 0.0 0.0 75.0 0 t 0 0.0 174.0 250.0 0.0 0.0 171.0 31.0 274.0 0
MA2173.1_shift4 (mef-2)				; positions_6nt_m2 versus MA2173.1 (mef-2); m=2/2; ncol2=7; w=0; offset=4; strand=D; shift=4; score=0.475956; ----AAAATA ; cor=; Ncor= a 0 0 0 0 422.0 517.0 501.0 516.0 9.0 514.0 c 0 0 0 0 26.0 9.0 15.0 11.0 7.0 12.0 g 0 0 0 0 80.0 27.0 26.0 8.0 12.0 19.0 t 0 0 0 0 30.0 5.0 16.0 23.0 530.0 13.0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 2 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; vwAAAATTCwr ; Alignment reference a 22 27 81 75 78 79 0 11 4 23 24 c 24 14 1 0 1 2 0 0 78 2 12 g 22 6 0 0 0 1 1 0 0 17 37 t 14 35 0 7 3 0 81 71 0 40 9
MA2179.1_rc_shift2 (ceh-10_rc)				; positions_6nt_m1 versus MA2179.1_rc (ceh-10_rc); m=1/1; ncol2=11; w=0; offset=2; strand=R; shift=2; score=0.500354; --AwAATTwdm ; cor=; Ncor= a 0 0 75.0 47.0 85.0 91.0 8.0 0.0 64.0 25.0 36.0 c 0 0 0.0 0.0 0.0 0.0 0.0 8.0 0.0 7.0 50.0 g 0 0 8.0 0.0 7.0 8.0 0.0 0.0 0.0 39.0 0.0 t 0 0 16.0 52.0 7.0 0.0 91.0 91.0 35.0 28.0 13.0