One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.174416_2025-05-16.174416_Ix0OVW/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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/2025/05/16/peak-motifs.2025-05-16.174416_2025-05-16.174416_Ix0OVW/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift1 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1) |
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; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -crCCTCAGCct
; Alignment reference
a 0 9 12 5 2 0 0 34 2 3 7 6
c 0 11 4 31 35 2 33 3 0 31 14 9
g 0 8 12 0 0 3 1 0 35 1 7 8
t 0 9 9 1 0 32 3 0 0 2 9 14
|
| oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1) |
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; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -crCCTCAGCct
; cor=; Ncor=
a 0 9 12 5 2 0 0 34 2 3 7 6
c 0 11 4 31 35 2 33 3 0 31 14 9
g 0 8 12 0 0 3 1 0 35 1 7 8
t 0 9 9 1 0 32 3 0 0 2 9 14
|
| oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc) |
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; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1_rc; m=2/2; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.735941; hdGCCTCAGsy-
; cor=; Ncor=
a 7 7 2 0 2 0 0 24 1 5 5 0
c 10 2 0 28 25 1 27 2 1 10 11 0
g 3 8 26 0 0 2 0 2 26 9 5 0
t 8 11 0 0 1 25 1 0 0 4 7 0
|
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift1 ; 3 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1) |
 |
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; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -rsCTGAGGChd
; Alignment reference
a 0 7 4 0 0 1 25 1 0 0 11 8
c 0 5 9 26 2 0 2 0 0 26 8 3
g 0 11 10 1 2 27 1 25 28 0 2 10
t 0 5 5 1 24 0 0 2 0 2 7 7
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| oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1) |
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; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -rsCTGAGGChd
; cor=; Ncor=
a 0 7 4 0 0 1 25 1 0 0 11 8
c 0 5 9 26 2 0 2 0 0 26 8 3
g 0 11 10 1 2 27 1 25 28 0 2 10
t 0 5 5 1 24 0 0 2 0 2 7 7
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| oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc) |
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; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1_rc; m=2/2; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.735941; agGCTGAGGyg-
; cor=; Ncor=
a 14 9 2 0 0 3 32 0 1 9 9 0
c 8 7 1 35 0 1 3 0 0 12 8 0
g 9 14 31 0 3 33 2 35 31 4 11 0
t 6 7 3 2 34 0 0 2 5 12 9 0
|
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |
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; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; dvCAGATGGkd
; Alignment reference
a 12 13 8 42 3 43 0 1 2 11 13
c 11 15 33 1 2 0 2 1 2 7 7
g 12 12 4 2 41 0 0 43 41 12 13
t 12 7 2 2 1 4 45 2 2 17 14
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| oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |
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; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; dvCAGATGGkd
; cor=; Ncor=
a 12 13 8 42 3 43 0 1 2 11 13
c 11 15 33 1 2 0 2 1 2 7 7
g 12 12 4 2 41 0 0 43 41 12 13
t 12 7 2 2 1 4 45 2 2 17 14
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