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_6nt_m3/peak-motifs_positions_6nt_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/2025/11/25/peak-motifs.2025-11-25.143236_2025-11-25.143236_C5OFib/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant
One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6nt_m3_shift0 (positions_6nt_m3) |
 |
|
|
; positions_6nt_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; wyAGGTTAACCTrw
; Alignment reference
a 364 296 1030 118 61 81 69 1131 1086 94 209 111 351 385
c 298 396 46 47 64 80 52 42 49 1080 926 110 255 254
g 254 257 109 922 1079 48 43 55 80 63 47 46 395 299
t 381 348 112 210 93 1088 1133 69 82 60 115 1030 296 359
|
| MA2001.2_shift7 (Six4) |
 |
|
|
; positions_6nt_m3 versus MA2001.2 (Six4); m=1/1; ncol2=7; w=0; offset=7; strand=D; shift=7; score=0.422354; -------AACCTGA
; cor=; Ncor=
a 0 0 0 0 0 0 0 4063.0 3970.0 209.0 480.0 202.0 124.0 4124.0
c 0 0 0 0 0 0 0 99.0 112.0 3506.0 3352.0 268.0 146.0 62.0
g 0 0 0 0 0 0 0 57.0 62.0 115.0 114.0 210.0 3906.0 52.0
t 0 0 0 0 0 0 0 72.0 147.0 461.0 345.0 3611.0 115.0 53.0
|