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.2025-06-19.093845_2025-06-19.093845_bSfSpH/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.2025-06-19.093845_2025-06-19.093845_bSfSpH/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB-plants.tab
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift6 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m1_shift6 (oligos_6-8nt_m1) |
 |
|
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; oligos_6-8nt_m1; m=0 (reference); ncol1=15; shift=6; ncol=21; ------scCGCCGCCGCCscC
; Alignment reference
a 0 0 0 0 0 0 15 8 5 7 4 3 5 3 2 9 4 2 16 14 5
c 0 0 0 0 0 0 32 74 105 14 105 104 10 103 107 11 105 110 51 70 83
g 0 0 0 0 0 0 64 19 0 94 3 5 99 6 4 92 2 2 43 11 18
t 0 0 0 0 0 0 4 14 5 0 3 3 1 3 2 3 4 1 5 20 9
|
One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift7 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m4_shift7 (oligos_6-8nt_m4) |
 |
|
|
; oligos_6-8nt_m4; m=0 (reference); ncol1=17; shift=7; ncol=24; -------CsCCsCCGCCGCCGCCs
; Alignment reference
a 0 0 0 0 0 0 0 6 18 5 5 9 3 5 7 5 4 7 5 1 9 8 6 21
c 0 0 0 0 0 0 0 88 36 99 104 48 110 111 12 114 111 15 110 115 16 105 94 33
g 0 0 0 0 0 0 0 18 62 10 7 62 4 4 103 1 6 100 2 4 94 4 9 63
t 0 0 0 0 0 0 0 12 8 10 8 5 7 4 2 4 3 2 7 4 5 7 15 7
|
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) |
 |
|
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; oligos_6-8nt_m2; m=0 (reference); ncol1=23; shift=4; ncol=27; ----CgCCsCCryCsCCGCCGCCGCCv
; Alignment reference
a 0 0 0 0 3 3 2 0 2 0 1 13 2 1 3 1 1 2 1 1 1 1 0 3 1 3 12
c 0 0 0 0 33 9 33 38 23 38 39 9 25 39 21 39 42 5 39 42 4 42 41 10 38 39 11
g 0 0 0 0 5 28 3 4 17 4 3 19 5 1 19 1 0 36 0 0 38 0 1 30 2 1 18
t 0 0 0 0 2 3 5 1 1 1 0 2 11 2 0 2 0 0 3 0 0 0 1 0 2 0 2
|
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=13; shift=1; ncol=14; -ssaCTGAGCCCym
; Alignment reference
a 0 2 3 16 1 0 0 27 0 2 0 0 6 7
c 0 17 9 5 23 2 0 0 2 23 27 23 10 12
g 0 8 13 3 3 1 26 0 25 2 0 4 3 4
t 0 0 2 3 0 24 1 0 0 0 0 0 8 4
|
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; yyACCCAGCCms
; Alignment reference
a 10 6 42 1 1 0 53 1 1 3 19 10
c 22 23 7 53 56 56 3 6 57 53 24 22
g 9 14 7 4 0 2 1 49 0 2 11 16
t 17 15 2 0 1 0 1 2 0 0 4 10
|