One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.153913_2026-02-26.153913_tNYaGF/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/2026/02/26/peak-motifs.2026-02-26.153913_2026-02-26.153913_tNYaGF/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6-7nt_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-7nt_m1_shift0 (oligos_6-7nt_m1)
; oligos_6-7nt_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; cmwaACCAAACsm ; Alignment reference a 2 3 3 3 9 0 0 8 9 9 0 2 3 c 3 3 0 2 0 9 9 0 0 0 9 3 6 g 2 1 2 2 0 0 0 0 0 0 0 3 0 t 2 2 4 2 0 0 0 1 0 0 0 1 0

oligos_6-7nt_m1_shift0 (oligos_6-7nt_m1)
; oligos_6-7nt_m1 versus oligos_6-7nt_m1; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; cmwaACCAAACsm ; cor=; Ncor= a 2 3 3 3 9 0 0 8 9 9 0 2 3 c 3 3 0 2 0 9 9 0 0 0 9 3 6 g 2 1 2 2 0 0 0 0 0 0 0 3 0 t 2 2 4 2 0 0 0 1 0 0 0 1 0

oligos_6-7nt_m8_shift0 (oligos_6-7nt_m8)
; oligos_6-7nt_m1 versus oligos_6-7nt_m8; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.973431; yhwmACCAAACsm ; cor=; Ncor= a 2 4 3 3 11 0 1 11 11 9 0 2 3 c 3 3 0 5 0 11 10 0 0 2 11 4 7 g 2 1 1 2 0 0 0 0 0 0 0 4 1 t 4 3 7 1 0 0 0 0 0 0 0 1 0

dyads_m2_shift2 (dyads_m2)
; oligos_6-7nt_m1 versus dyads_m2; m=3/3; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.628821; --tyACCwAmCGC ; cor=; Ncor= a 0 0 1 1 6 0 0 4 6 3 0 0 0 c 0 0 0 3 0 6 6 0 0 3 6 0 6 g 0 0 1 0 0 0 0 0 0 0 0 6 0 t 0 0 4 2 0 0 0 2 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6-7nt_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-7nt_m2_shift0 (oligos_6-7nt_m2)
; oligos_6-7nt_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; yrCCACCGTbw ; Alignment reference a 0 3 0 0 8 0 0 1 1 0 4 c 6 1 8 9 0 9 9 0 1 3 0 g 0 3 1 0 1 0 0 8 0 3 2 t 3 2 0 0 0 0 0 0 7 3 3

oligos_6-7nt_m2_shift0 (oligos_6-7nt_m2)
; oligos_6-7nt_m2 versus oligos_6-7nt_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; yrCCACCGTbw ; cor=; Ncor= a 0 3 0 0 8 0 0 1 1 0 4 c 6 1 8 9 0 9 9 0 1 3 0 g 0 3 1 0 1 0 0 8 0 3 2 t 3 2 0 0 0 0 0 0 7 3 3

dyads_m1_shift0 (dyads_m1)
; oligos_6-7nt_m2 versus dyads_m1; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.876232; CsCCACCGwb- ; cor=; Ncor= a 1 2 0 0 7 0 0 0 3 0 0 c 7 3 10 9 0 10 10 0 2 3 0 g 0 3 0 0 2 0 0 10 0 4 0 t 2 2 0 1 1 0 0 0 5 3 0

One-to-n matrix alignment; reference matrix: oligos_6-7nt_m7_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-7nt_m7_shift0 (oligos_6-7nt_m7)
; oligos_6-7nt_m7; m=0 (reference); ncol1=12; shift=0; ncol=12; wAACGSCGTTwa ; Alignment reference a 3 5 6 0 0 0 0 0 0 0 3 4 c 1 1 1 7 0 5 7 0 0 1 0 1 g 0 1 0 0 7 2 0 6 0 0 1 1 t 3 0 0 0 0 0 0 1 7 6 3 1

oligos_6-7nt_m7_shift0 (oligos_6-7nt_m7)
; oligos_6-7nt_m7 versus oligos_6-7nt_m7; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; wAACGSCGTTwa ; cor=; Ncor= a 3 5 6 0 0 0 0 0 0 0 3 4 c 1 1 1 7 0 5 7 0 0 1 0 1 g 0 1 0 0 7 2 0 6 0 0 1 1 t 3 0 0 0 0 0 0 1 7 6 3 1

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=26; shift=0; ncol=26; mmTCAhhmawthhwkwhahwwACAww ; Alignment reference a 4 5 0 0 11 4 3 7 6 6 1 4 3 3 2 5 3 7 3 8 7 12 0 12 4 4 c 4 5 0 12 0 3 3 3 2 1 2 3 4 2 2 2 6 1 3 1 1 0 12 0 2 2 g 2 0 0 0 1 2 2 0 2 0 2 0 1 2 3 2 0 2 1 0 1 0 0 0 1 1 t 2 2 12 0 0 3 4 2 2 5 7 5 4 5 5 3 3 2 5 3 3 0 0 0 5 5

dyads_m3_shift0 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/1; ncol2=26; w=0; offset=0; strand=D; shift=0; score= 1; mmTCAhhmawthhwkwhahwwACAww ; cor=; Ncor= a 4 5 0 0 11 4 3 7 6 6 1 4 3 3 2 5 3 7 3 8 7 12 0 12 4 4 c 4 5 0 12 0 3 3 3 2 1 2 3 4 2 2 2 6 1 3 1 1 0 12 0 2 2 g 2 0 0 0 1 2 2 0 2 0 2 0 1 2 3 2 0 2 1 0 1 0 0 0 1 1 t 2 2 12 0 0 3 4 2 2 5 7 5 4 5 5 3 3 2 5 3 3 0 0 0 5 5

One-to-n matrix alignment; reference matrix: oligos_6-7nt_m8_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-7nt_m8_shift0 (oligos_6-7nt_m8)
; oligos_6-7nt_m8; m=0 (reference); ncol1=13; shift=0; ncol=13; yhwmACCAAACsm ; Alignment reference a 2 4 3 3 11 0 1 11 11 9 0 2 3 c 3 3 0 5 0 11 10 0 0 2 11 4 7 g 2 1 1 2 0 0 0 0 0 0 0 4 1 t 4 3 7 1 0 0 0 0 0 0 0 1 0

oligos_6-7nt_m8_shift0 (oligos_6-7nt_m8)
; oligos_6-7nt_m8 versus oligos_6-7nt_m8; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; yhwmACCAAACsm ; cor=; Ncor= a 2 4 3 3 11 0 1 11 11 9 0 2 3 c 3 3 0 5 0 11 10 0 0 2 11 4 7 g 2 1 1 2 0 0 0 0 0 0 0 4 1 t 4 3 7 1 0 0 0 0 0 0 0 1 0

oligos_6-7nt_m1_shift0 (oligos_6-7nt_m1)
; oligos_6-7nt_m8 versus oligos_6-7nt_m1; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.973431; cmwaACCAAACsm ; cor=; Ncor= a 2 3 3 3 9 0 0 8 9 9 0 2 3 c 3 3 0 2 0 9 9 0 0 0 9 3 6 g 2 1 2 2 0 0 0 0 0 0 0 3 0 t 2 2 4 2 0 0 0 1 0 0 0 1 0

dyads_m2_shift2 (dyads_m2)
; oligos_6-7nt_m8 versus dyads_m2; m=3/3; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.648957; --tyACCwAmCGC ; cor=; Ncor= a 0 0 1 1 6 0 0 4 6 3 0 0 0 c 0 0 0 3 0 6 6 0 0 3 6 0 6 g 0 0 1 0 0 0 0 0 0 0 0 6 0 t 0 0 4 2 0 0 0 2 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; CsCCACCGwb ; Alignment reference a 1 2 0 0 7 0 0 0 3 0 c 7 3 10 9 0 10 10 0 2 3 g 0 3 0 0 2 0 0 10 0 4 t 2 2 0 1 1 0 0 0 5 3

dyads_m1_shift0 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; CsCCACCGwb ; cor=; Ncor= a 1 2 0 0 7 0 0 0 3 0 c 7 3 10 9 0 10 10 0 2 3 g 0 3 0 0 2 0 0 10 0 4 t 2 2 0 1 1 0 0 0 5 3

oligos_6-7nt_m2_shift0 (oligos_6-7nt_m2)
; dyads_m1 versus oligos_6-7nt_m2; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.876232; yrCCACCGTb ; cor=; Ncor= a 0 3 0 0 8 0 0 1 1 0 c 6 1 8 9 0 9 9 0 1 3 g 0 3 1 0 1 0 0 8 0 3 t 3 2 0 0 0 0 0 0 7 3

One-to-n matrix alignment; reference matrix: oligos_6-7nt_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-7nt_m5_shift0 (oligos_6-7nt_m5)
; oligos_6-7nt_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; ryCAGCCACsA ; Alignment reference a 3 1 0 5 1 0 0 6 0 0 5 c 1 3 6 0 0 6 6 0 6 3 0 g 2 0 0 0 5 0 0 0 0 2 1 t 0 2 0 1 0 0 0 0 0 1 0

oligos_6-7nt_m5_shift0 (oligos_6-7nt_m5)
; oligos_6-7nt_m5 versus oligos_6-7nt_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; ryCAGCCACsA ; cor=; Ncor= a 3 1 0 5 1 0 0 6 0 0 5 c 1 3 6 0 0 6 6 0 6 3 0 g 2 0 0 0 5 0 0 0 0 2 1 t 0 2 0 1 0 0 0 0 0 1 0

oligos_6-7nt_m4_shift3 (oligos_6-7nt_m4)
; oligos_6-7nt_m5 versus oligos_6-7nt_m4; m=2/2; ncol2=11; w=0; offset=3; strand=D; shift=3; score=0.504845; ---ArCCACGA ; cor=; Ncor= a 0 0 0 4 2 0 0 5 0 0 5 c 0 0 0 0 0 5 5 0 5 0 0 g 0 0 0 1 2 0 0 0 0 5 0 t 0 0 0 0 1 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6-7nt_m10_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-7nt_m10_shift0 (oligos_6-7nt_m10)
; oligos_6-7nt_m10; m=0 (reference); ncol1=11; shift=0; ncol=11; svCTTTTAChw ; Alignment reference a 1 2 0 0 0 1 0 7 0 3 3 c 3 2 7 0 0 0 0 0 7 2 0 g 2 3 0 1 0 0 0 0 0 0 1 t 1 0 0 6 7 6 7 0 0 2 3

oligos_6-7nt_m10_shift0 (oligos_6-7nt_m10)
; oligos_6-7nt_m10 versus oligos_6-7nt_m10; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; svCTTTTAChw ; cor=; Ncor= a 1 2 0 0 0 1 0 7 0 3 3 c 3 2 7 0 0 0 0 0 7 2 0 g 2 3 0 1 0 0 0 0 0 0 1 t 1 0 0 6 7 6 7 0 0 2 3

oligos_6-7nt_m6_rc_shift3 (oligos_6-7nt_m6_rc)
; oligos_6-7nt_m10 versus oligos_6-7nt_m6_rc; m=2/2; ncol2=11; w=0; offset=3; strand=R; shift=3; score=0.418126; ---cdTTACTA ; cor=; Ncor= a 0 0 0 2 3 0 0 9 0 0 8 c 0 0 0 4 0 0 0 0 8 1 0 g 0 0 0 1 3 0 0 0 0 1 0 t 0 0 0 2 3 9 9 0 1 7 1

One-to-n matrix alignment; reference matrix: oligos_6-7nt_m6_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-7nt_m6_shift0 (oligos_6-7nt_m6)
; oligos_6-7nt_m6; m=0 (reference); ncol1=11; shift=0; ncol=11; agGTAGTAAhg ; Alignment reference a 5 2 1 1 7 1 0 9 9 3 2 c 2 2 0 0 1 0 0 0 0 3 1 g 2 3 8 0 1 8 0 0 0 0 4 t 0 2 0 8 0 0 9 0 0 3 2

oligos_6-7nt_m6_shift0 (oligos_6-7nt_m6)
; oligos_6-7nt_m6 versus oligos_6-7nt_m6; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; agGTAGTAAhg ; cor=; Ncor= a 5 2 1 1 7 1 0 9 9 3 2 c 2 2 0 0 1 0 0 0 0 3 1 g 2 3 8 0 1 8 0 0 0 0 4 t 0 2 0 8 0 0 9 0 0 3 2

oligos_6-7nt_m10_rc_shift3 (oligos_6-7nt_m10_rc)
; oligos_6-7nt_m6 versus oligos_6-7nt_m10_rc; m=2/2; ncol2=11; w=0; offset=3; strand=R; shift=3; score=0.418126; ---wdGTAAAA ; cor=; Ncor= a 0 0 0 3 2 0 0 7 6 7 6 c 0 0 0 1 0 0 0 0 0 0 1 g 0 0 0 0 2 7 0 0 0 0 0 t 0 0 0 3 3 0 7 0 1 0 0

One-to-n matrix alignment; reference matrix: dyads_m2_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift2 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=13; shift=2; ncol=15; --tyACCwAmCGCva ; Alignment reference a 0 0 1 1 6 0 0 4 6 3 0 0 0 2 3 c 0 0 0 3 0 6 6 0 0 3 6 0 6 2 1 g 0 0 1 0 0 0 0 0 0 0 0 6 0 2 1 t 0 0 4 2 0 0 0 2 0 0 0 0 0 0 1

dyads_m2_shift2 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --tyACCwAmCGCva ; cor=; Ncor= a 0 0 1 1 6 0 0 4 6 3 0 0 0 2 3 c 0 0 0 3 0 6 6 0 0 3 6 0 6 2 1 g 0 0 1 0 0 0 0 0 0 0 0 6 0 2 1 t 0 0 4 2 0 0 0 2 0 0 0 0 0 0 1

oligos_6-7nt_m8_shift0 (oligos_6-7nt_m8)
; dyads_m2 versus oligos_6-7nt_m8; m=2/3; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.648957; yhwmACCAAACsm-- ; cor=; Ncor= a 2 4 3 3 11 0 1 11 11 9 0 2 3 0 0 c 3 3 0 5 0 11 10 0 0 2 11 4 7 0 0 g 2 1 1 2 0 0 0 0 0 0 0 4 1 0 0 t 4 3 7 1 0 0 0 0 0 0 0 1 0 0 0

oligos_6-7nt_m1_shift0 (oligos_6-7nt_m1)
; dyads_m2 versus oligos_6-7nt_m1; m=3/3; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.628821; cmwaACCAAACsm-- ; cor=; Ncor= a 2 3 3 3 9 0 0 8 9 9 0 2 3 0 0 c 3 3 0 2 0 9 9 0 0 0 9 3 6 0 0 g 2 1 2 2 0 0 0 0 0 0 0 3 0 0 0 t 2 2 4 2 0 0 0 1 0 0 0 1 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6-7nt_m4_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-7nt_m4_shift3 (oligos_6-7nt_m4)
; oligos_6-7nt_m4; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ArCCACGAmww ; Alignment reference a 0 0 0 4 2 0 0 5 0 0 5 2 2 2 c 0 0 0 0 0 5 5 0 5 0 0 3 1 0 g 0 0 0 1 2 0 0 0 0 5 0 0 0 0 t 0 0 0 0 1 0 0 0 0 0 0 0 2 3

oligos_6-7nt_m4_shift3 (oligos_6-7nt_m4)
; oligos_6-7nt_m4 versus oligos_6-7nt_m4; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=3; score= 1; ---ArCCACGAmww ; cor=; Ncor= a 0 0 0 4 2 0 0 5 0 0 5 2 2 2 c 0 0 0 0 0 5 5 0 5 0 0 3 1 0 g 0 0 0 1 2 0 0 0 0 5 0 0 0 0 t 0 0 0 0 1 0 0 0 0 0 0 0 2 3

oligos_6-7nt_m5_shift0 (oligos_6-7nt_m5)
; oligos_6-7nt_m4 versus oligos_6-7nt_m5; m=2/2; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.504845; ryCAGCCACsA--- ; cor=; Ncor= a 3 1 0 5 1 0 0 6 0 0 5 0 0 0 c 1 3 6 0 0 6 6 0 6 3 0 0 0 0 g 2 0 0 0 5 0 0 0 0 2 1 0 0 0 t 0 2 0 1 0 0 0 0 0 1 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6-7nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-7nt_m3_shift0 (oligos_6-7nt_m3)
; oligos_6-7nt_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; mrAGAGATCTcTyk ; Alignment reference a 3 5 8 2 10 0 10 0 1 1 1 0 2 2 c 4 1 1 0 0 0 1 0 9 0 7 2 3 1 g 2 3 2 8 0 10 0 1 1 0 1 1 2 4 t 2 2 0 1 1 1 0 10 0 10 2 8 4 4

oligos_6-7nt_m3_shift0 (oligos_6-7nt_m3)
; oligos_6-7nt_m3 versus oligos_6-7nt_m3; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; mrAGAGATCTcTyk ; cor=; Ncor= a 3 5 8 2 10 0 10 0 1 1 1 0 2 2 c 4 1 1 0 0 0 1 0 9 0 7 2 3 1 g 2 3 2 8 0 10 0 1 1 0 1 1 2 4 t 2 2 0 1 1 1 0 10 0 10 2 8 4 4

One-to-n matrix alignment; reference matrix: oligos_6-7nt_m9_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6-7nt_m9_shift0 (oligos_6-7nt_m9)
; oligos_6-7nt_m9; m=0 (reference); ncol1=11; shift=0; ncol=11; dmSATGGCYmd ; Alignment reference a 3 2 0 8 0 0 0 0 0 2 3 c 0 4 6 0 0 0 0 7 6 4 0 g 2 1 2 0 0 8 8 0 0 1 2 t 3 1 0 0 8 0 0 1 2 1 3

oligos_6-7nt_m9_shift0 (oligos_6-7nt_m9)
; oligos_6-7nt_m9 versus oligos_6-7nt_m9; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; dmSATGGCYmd ; cor=; Ncor= a 3 2 0 8 0 0 0 0 0 2 3 c 0 4 6 0 0 0 0 7 6 4 0 g 2 1 2 0 0 8 8 0 0 1 2 t 3 1 0 0 8 0 0 1 2 1 3

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-7nt_m1_shift0 (oligos_6-7nt_m1)				; oligos_6-7nt_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; cmwaACCAAACsm ; Alignment reference a 2 3 3 3 9 0 0 8 9 9 0 2 3 c 3 3 0 2 0 9 9 0 0 0 9 3 6 g 2 1 2 2 0 0 0 0 0 0 0 3 0 t 2 2 4 2 0 0 0 1 0 0 0 1 0
oligos_6-7nt_m1_shift0 (oligos_6-7nt_m1)				; oligos_6-7nt_m1 versus oligos_6-7nt_m1; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; cmwaACCAAACsm ; cor=; Ncor= a 2 3 3 3 9 0 0 8 9 9 0 2 3 c 3 3 0 2 0 9 9 0 0 0 9 3 6 g 2 1 2 2 0 0 0 0 0 0 0 3 0 t 2 2 4 2 0 0 0 1 0 0 0 1 0
oligos_6-7nt_m8_shift0 (oligos_6-7nt_m8)				; oligos_6-7nt_m1 versus oligos_6-7nt_m8; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.973431; yhwmACCAAACsm ; cor=; Ncor= a 2 4 3 3 11 0 1 11 11 9 0 2 3 c 3 3 0 5 0 11 10 0 0 2 11 4 7 g 2 1 1 2 0 0 0 0 0 0 0 4 1 t 4 3 7 1 0 0 0 0 0 0 0 1 0
dyads_m2_shift2 (dyads_m2)				; oligos_6-7nt_m1 versus dyads_m2; m=3/3; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.628821; --tyACCwAmCGC ; cor=; Ncor= a 0 0 1 1 6 0 0 4 6 3 0 0 0 c 0 0 0 3 0 6 6 0 0 3 6 0 6 g 0 0 1 0 0 0 0 0 0 0 0 6 0 t 0 0 4 2 0 0 0 2 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6-7nt_m8_shift0 (oligos_6-7nt_m8)				; oligos_6-7nt_m8; m=0 (reference); ncol1=13; shift=0; ncol=13; yhwmACCAAACsm ; Alignment reference a 2 4 3 3 11 0 1 11 11 9 0 2 3 c 3 3 0 5 0 11 10 0 0 2 11 4 7 g 2 1 1 2 0 0 0 0 0 0 0 4 1 t 4 3 7 1 0 0 0 0 0 0 0 1 0
oligos_6-7nt_m8_shift0 (oligos_6-7nt_m8)				; oligos_6-7nt_m8 versus oligos_6-7nt_m8; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; yhwmACCAAACsm ; cor=; Ncor= a 2 4 3 3 11 0 1 11 11 9 0 2 3 c 3 3 0 5 0 11 10 0 0 2 11 4 7 g 2 1 1 2 0 0 0 0 0 0 0 4 1 t 4 3 7 1 0 0 0 0 0 0 0 1 0
oligos_6-7nt_m1_shift0 (oligos_6-7nt_m1)				; oligos_6-7nt_m8 versus oligos_6-7nt_m1; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.973431; cmwaACCAAACsm ; cor=; Ncor= a 2 3 3 3 9 0 0 8 9 9 0 2 3 c 3 3 0 2 0 9 9 0 0 0 9 3 6 g 2 1 2 2 0 0 0 0 0 0 0 3 0 t 2 2 4 2 0 0 0 1 0 0 0 1 0
dyads_m2_shift2 (dyads_m2)				; oligos_6-7nt_m8 versus dyads_m2; m=3/3; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.648957; --tyACCwAmCGC ; cor=; Ncor= a 0 0 1 1 6 0 0 4 6 3 0 0 0 c 0 0 0 3 0 6 6 0 0 3 6 0 6 g 0 0 1 0 0 0 0 0 0 0 0 6 0 t 0 0 4 2 0 0 0 2 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift2 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=13; shift=2; ncol=15; --tyACCwAmCGCva ; Alignment reference a 0 0 1 1 6 0 0 4 6 3 0 0 0 2 3 c 0 0 0 3 0 6 6 0 0 3 6 0 6 2 1 g 0 0 1 0 0 0 0 0 0 0 0 6 0 2 1 t 0 0 4 2 0 0 0 2 0 0 0 0 0 0 1
dyads_m2_shift2 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=2; score= 1; --tyACCwAmCGCva ; cor=; Ncor= a 0 0 1 1 6 0 0 4 6 3 0 0 0 2 3 c 0 0 0 3 0 6 6 0 0 3 6 0 6 2 1 g 0 0 1 0 0 0 0 0 0 0 0 6 0 2 1 t 0 0 4 2 0 0 0 2 0 0 0 0 0 0 1
oligos_6-7nt_m8_shift0 (oligos_6-7nt_m8)				; dyads_m2 versus oligos_6-7nt_m8; m=2/3; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.648957; yhwmACCAAACsm-- ; cor=; Ncor= a 2 4 3 3 11 0 1 11 11 9 0 2 3 0 0 c 3 3 0 5 0 11 10 0 0 2 11 4 7 0 0 g 2 1 1 2 0 0 0 0 0 0 0 4 1 0 0 t 4 3 7 1 0 0 0 0 0 0 0 1 0 0 0
oligos_6-7nt_m1_shift0 (oligos_6-7nt_m1)				; dyads_m2 versus oligos_6-7nt_m1; m=3/3; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.628821; cmwaACCAAACsm-- ; cor=; Ncor= a 2 3 3 3 9 0 0 8 9 9 0 2 3 0 0 c 3 3 0 2 0 9 9 0 0 0 9 3 6 0 0 g 2 1 2 2 0 0 0 0 0 0 0 3 0 0 0 t 2 2 4 2 0 0 0 1 0 0 0 1 0 0 0