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.2025-06-19.092322_2025-06-19.092322_shBOom/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.2025-06-19.092322_2025-06-19.092322_shBOom/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB-plants.tab
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift8 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m4_shift8 (oligos_6-8nt_m4) |
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; oligos_6-8nt_m4; m=0 (reference); ncol1=10; shift=8; ncol=18; --------bsGCCGGCsv
; Alignment reference
a 0 0 0 0 0 0 0 0 15 24 0 0 0 0 0 0 20 25
c 0 0 0 0 0 0 0 0 31 25 0 98 98 0 0 98 29 27
g 0 0 0 0 0 0 0 0 27 29 98 0 0 98 98 0 25 31
t 0 0 0 0 0 0 0 0 25 20 0 0 0 0 0 0 24 15
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One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift1 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m3_shift1 (oligos_6-8nt_m3) |
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; oligos_6-8nt_m3; m=0 (reference); ncol1=12; shift=1; ncol=13; -cgCCAGCAGCms
; Alignment reference
a 0 20 33 3 6 129 6 3 119 5 1 36 21
c 0 60 32 113 127 5 6 137 7 4 131 38 46
g 0 34 47 21 6 3 125 2 9 133 6 35 52
t 0 28 30 5 3 5 5 0 7 0 4 33 23
|
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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; oligos_6-8nt_m1; m=0 (reference); ncol1=12; shift=4; ncol=16; ----ccCCCCGCCCcy
; Alignment reference
a 0 0 0 0 32 37 9 4 6 3 6 4 5 9 40 31
c 0 0 0 0 81 87 179 190 183 179 50 192 185 182 89 91
g 0 0 0 0 50 44 6 5 10 8 144 5 8 10 33 30
t 0 0 0 0 40 35 9 4 4 13 3 2 5 2 41 51
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift2 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2) |
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; oligos_6-8nt_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --drTAcATAtay
; Alignment reference
a 0 0 41 39 3 131 9 112 1 133 24 46 34
c 0 0 27 31 0 5 87 7 0 5 29 26 36
g 0 0 35 37 7 0 15 12 0 0 29 33 32
t 0 0 36 32 129 3 28 8 138 1 57 34 37
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift0 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5) |
 |
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; oligos_6-8nt_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; gyAGACCTTGcs
; Alignment reference
a 15 11 53 1 51 3 5 1 1 1 13 13
c 15 24 2 3 4 55 51 3 1 0 23 19
g 21 10 3 56 5 3 3 2 2 59 11 18
t 10 16 3 1 1 0 2 55 57 1 14 11
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