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.2025-06-19.093641_2025-06-19.093641_ZnDYv6/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.2025-06-19.093641_2025-06-19.093641_ZnDYv6/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB-plants.tab
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift5 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m1_shift5 (oligos_6-8nt_m1) |
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; oligos_6-8nt_m1; m=0 (reference); ncol1=12; shift=5; ncol=17; -----cvCACACGCCcr
; Alignment reference
a 0 0 0 0 0 8 14 2 40 1 46 0 7 0 9 8 17
c 0 0 0 0 0 24 15 42 6 49 3 49 0 50 37 24 5
g 0 0 0 0 0 9 14 3 3 0 1 0 43 0 4 11 18
t 0 0 0 0 0 9 7 3 1 0 0 1 0 0 0 7 10
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift3 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m4_shift3 (oligos_6-8nt_m4) |
 |
|
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; oligos_6-8nt_m4; m=0 (reference); ncol1=10; shift=3; ncol=13; ---sbCCTGGCmy
; Alignment reference
a 0 0 0 5 6 0 0 0 0 0 0 13 7
c 0 0 0 14 13 42 42 0 0 0 42 13 14
g 0 0 0 17 12 0 0 0 42 42 0 10 10
t 0 0 0 6 11 0 0 42 0 0 0 6 11
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift8 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m5_shift8 (oligos_6-8nt_m5) |
 |
|
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; oligos_6-8nt_m5; m=0 (reference); ncol1=14; shift=8; ncol=22; --------svCaCACACGCccr
; Alignment reference
a 0 0 0 0 0 0 0 0 7 13 2 27 1 40 1 43 0 7 1 8 4 18
c 0 0 0 0 0 0 0 0 21 13 37 8 37 3 44 3 47 2 44 29 23 6
g 0 0 0 0 0 0 0 0 14 12 5 7 4 4 1 0 0 38 0 6 10 13
t 0 0 0 0 0 0 0 0 5 9 3 5 5 0 1 1 0 0 2 4 10 10
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift2 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m3_shift2 (oligos_6-8nt_m3) |
 |
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; oligos_6-8nt_m3; m=0 (reference); ncol1=11; shift=2; ncol=13; --tsCATAATAgg
; Alignment reference
a 0 0 11 7 0 41 1 42 38 3 43 11 10
c 0 0 8 12 42 1 1 2 4 5 1 9 11
g 0 0 9 16 3 3 2 0 2 1 1 18 17
t 0 0 18 11 1 1 42 2 2 37 1 8 8
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift0 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2) |
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; oligos_6-8nt_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; cmCACACGCACGcw
; Alignment reference
a 6 14 2 29 0 37 0 4 2 31 0 3 4 14
c 26 14 32 4 39 1 39 5 38 2 37 3 20 9
g 5 8 5 6 2 2 1 32 1 5 3 34 8 6
t 4 5 2 2 0 1 1 0 0 3 1 1 9 12
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