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.2025-06-19.091816_2025-06-19.091816_x3rpdD/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.2025-06-19.091816_2025-06-19.091816_x3rpdD/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB-plants.tab
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=10; shift=1; ncol=11; -skGCACGCvs
; Alignment reference
a 0 27 25 0 0 125 0 0 0 35 22
c 0 41 25 0 125 0 125 0 125 35 36
g 0 32 36 125 0 0 0 125 0 34 38
t 0 25 39 0 0 0 0 0 0 21 29
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One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift12 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m4_shift12 (oligos_6-8nt_m4) |
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; oligos_6-8nt_m4; m=0 (reference); ncol1=13; shift=12; ncol=25; ------------cssCCGCCGCCss
; Alignment reference
a 0 0 0 0 0 0 0 0 0 0 0 0 32 21 31 5 5 5 2 2 7 7 10 35 32
c 0 0 0 0 0 0 0 0 0 0 0 0 59 60 55 141 142 9 142 141 14 137 136 55 51
g 0 0 0 0 0 0 0 0 0 0 0 0 35 43 45 5 4 141 9 7 136 6 4 48 43
t 0 0 0 0 0 0 0 0 0 0 0 0 31 33 26 6 6 2 4 7 0 7 7 19 31
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One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift9 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m1_shift9 (oligos_6-8nt_m1) |
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; oligos_6-8nt_m1; m=0 (reference); ncol1=11; shift=9; ncol=20; ---------ssCCAACCcss
; Alignment reference
a 0 0 0 0 0 0 0 0 0 24 29 3 1 113 122 0 0 13 15 25
c 0 0 0 0 0 0 0 0 0 38 42 116 113 1 1 120 119 76 45 33
g 0 0 0 0 0 0 0 0 0 32 34 3 8 9 0 1 4 20 45 42
t 0 0 0 0 0 0 0 0 0 31 20 3 3 2 2 4 2 16 20 25
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One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift9 ; 1 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6-8nt_m5_shift9 (oligos_6-8nt_m5) |
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; oligos_6-8nt_m5; m=0 (reference); ncol1=12; shift=9; ncol=21; ---------csCCACGCCCcc
; Alignment reference
a 0 0 0 0 0 0 0 0 0 26 17 1 1 123 9 9 3 6 4 36 30
c 0 0 0 0 0 0 0 0 0 62 67 141 152 14 124 4 138 142 146 65 56
g 0 0 0 0 0 0 0 0 0 38 40 11 2 9 13 136 13 4 2 31 31
t 0 0 0 0 0 0 0 0 0 29 31 2 0 9 9 6 1 3 3 23 38
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