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_m5/peak-motifs_positions_6nt_m5.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_m5/peak-motifs_positions_6nt_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant
One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift1 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6nt_m5_shift1 (positions_6nt_m5) |
 |
|
|
; positions_6nt_m5; m=0 (reference); ncol1=12; shift=1; ncol=13; -csGtCGCGaCsg
; Alignment reference
a 0 272 221 187 102 79 63 68 35 823 83 250 233
c 0 481 371 106 217 1034 91 1061 127 132 894 430 295
g 0 293 430 901 131 128 1052 88 1035 215 111 373 481
t 0 231 255 83 827 36 71 60 80 107 189 224 268
|
| MA0749.2_rc_shift0 (ZBED1_rc) |
 |
|
|
; positions_6nt_m5 versus MA0749.2_rc (ZBED1_rc); m=1/2; ncol2=12; w=-1; offset=-1; strand=R; shift=0; score=0.64978; yATGTCGCGAyA-
; cor=; Ncor=
a 608.0 5055.0 144.0 865.0 0.0 0.0 110.0 2.0 18.0 5510.0 8.0 5321.0 0
c 1876.0 635.0 10.0 0.0 12.0 6013.0 0.0 5979.0 6.0 0.0 2065.0 56.0 0
g 270.0 273.0 11.0 4330.0 9.0 4.0 5357.0 3.0 5373.0 8.0 15.0 22.0 0
t 3123.0 118.0 5276.0 6.0 5326.0 4.0 4.0 127.0 0.0 6.0 3841.0 441.0 0
|
| MA1995.2_rc_shift3 (Npas4_rc) |
 |
|
|
; positions_6nt_m5 versus MA1995.2_rc (Npas4_rc); m=2/2; ncol2=7; w=0; offset=2; strand=R; shift=3; score=0.436912; ---GTCACGA---
; cor=; Ncor=
a 0 0 0 617.0 511.0 118.0 8479.0 126.0 333.0 7226.0 0 0 0
c 0 0 0 647.0 367.0 8602.0 251.0 7969.0 580.0 702.0 0 0 0
g 0 0 0 7292.0 622.0 184.0 106.0 350.0 7713.0 492.0 0 0 0
t 0 0 0 404.0 7460.0 56.0 124.0 515.0 334.0 540.0 0 0 0
|