One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -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/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB-plants.tab
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift4 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m1_shift4 (oligos_6-8nt_m1) |
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|
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; oligos_6-8nt_m1; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wrCGTACTAyg
; Alignment reference
a 0 0 0 0 9 11 0 0 1 26 0 2 28 3 7
c 0 0 0 0 7 4 27 0 0 0 22 0 0 12 4
g 0 0 0 0 3 12 0 29 0 4 4 2 2 7 14
t 0 0 0 0 11 3 3 1 29 0 4 26 0 8 5
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift4 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m2_shift4 (oligos_6-8nt_m2) |
 |
|
|
; oligos_6-8nt_m2; m=0 (reference); ncol1=12; shift=4; ncol=16; ----cmAAACGCGAsw
; Alignment reference
a 0 0 0 0 3 6 16 17 16 1 1 0 0 14 3 5
c 0 0 0 0 6 5 0 0 0 15 0 15 0 1 6 3
g 0 0 0 0 4 3 0 0 1 1 16 2 17 1 5 2
t 0 0 0 0 4 3 1 0 0 0 0 0 0 1 3 7
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift2 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m5_shift2 (oligos_6-8nt_m5) |
 |
|
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; oligos_6-8nt_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --ycATCCCGCsc
; Alignment reference
a 0 0 9 7 39 1 1 0 3 0 1 4 11
c 0 0 13 18 4 0 43 42 40 3 36 21 16
g 0 0 9 10 1 0 0 2 2 38 8 13 10
t 0 0 14 10 1 44 1 1 0 4 0 7 8
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift0 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3) |
 |
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; oligos_6-8nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; ssACGACCGTgb
; Alignment reference
a 3 4 16 0 1 17 1 0 0 1 2 1
c 7 7 0 15 1 1 17 18 1 1 4 7
g 7 6 1 2 16 0 0 0 17 1 8 5
t 1 1 1 1 0 0 0 0 0 15 4 5
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift0 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4) |
 |
|
|
; oligos_6-8nt_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; yvAATAGCATGts
; Alignment reference
a 2 6 19 20 0 21 3 3 19 2 2 5 3
c 9 8 0 0 0 1 1 17 0 2 2 5 8
g 5 6 3 1 2 0 18 0 2 2 17 5 8
t 6 2 0 1 20 0 0 2 1 16 1 7 3
|