One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.203737_2025-04-28.203737_n2namY/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/2025/04/28/peak-motifs.2025-04-28.203737_2025-04-28.203737_n2namY/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: dyads_m1_shift3 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift3 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=24; shift=3; ncol=27; ---kyCGmTACwATCGATwGTAkCGrm ; Alignment reference a 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4

oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1)
; dyads_m1 versus oligos_6nt_mkv2_m1; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---kyCGmTACwATCGATwGTAkCGrm ; cor=; Ncor= a 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4

dyads_m1_shift3 (dyads_m1)
; dyads_m1 versus dyads_m1; m=2/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---kyCGmTACwATCGATwGTAkCGrm ; cor=; Ncor= a 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4

oligos_7nt_mkv2_m1_shift3 (oligos_7nt_mkv2_m1)
; dyads_m1 versus oligos_7nt_mkv2_m1; m=3/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.991257; ---stCGmTActATCGATagTAkCGas ; cor=; Ncor= a 0 0 0 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 c 0 0 0 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 g 0 0 0 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 t 0 0 0 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3

oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)
; dyads_m1 versus oligos_7nt_mkv2_m5_rc; m=4/10; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.905742; ----tcGaTActATCGATAgTAtCGag ; cor=; Ncor= a 0 0 0 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 3 0 2 8 4 c 0 0 0 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 0 15 1 2 4 g 0 0 0 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 4 1 14 4 5 t 0 0 0 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4 10 1 0 3 4

dyads_m7_shift2 (dyads_m7)
; dyads_m1 versus dyads_m7; m=5/10; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.864696; --wswCGATAsTATCGATwstwdYrw- ; cor=; Ncor= a 0 0 5 2 3 0 2 9 1 11 0 1 11 1 0 0 10 1 7 0 1 8 3 0 3 6 0 c 0 0 1 4 2 11 0 2 0 1 5 0 0 1 12 0 0 1 1 5 2 0 0 9 0 0 0 g 0 0 2 4 0 0 10 0 0 0 7 0 1 0 0 12 1 1 1 6 2 0 3 0 8 1 0 t 0 0 4 2 7 1 0 1 11 0 0 11 0 10 0 0 1 9 3 1 7 4 6 3 1 5 0

oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2_rc)
; dyads_m1 versus oligos_6nt_mkv2_m2_rc; m=6/10; ncol2=21; w=-1; offset=-1; strand=R; shift=2; score=0.681035; --daTCGATAsTATCGAtrkwws---- ; cor=; Ncor= a 0 0 6 11 2 0 1 21 0 22 1 2 21 1 0 1 16 3 7 5 6 6 5 0 0 0 0 c 0 0 5 3 2 21 0 1 0 0 14 0 2 0 22 0 1 5 4 4 3 3 7 0 0 0 0 g 0 0 6 5 3 1 22 0 2 1 7 0 0 0 0 22 4 2 8 8 4 4 7 0 0 0 0 t 0 0 6 4 16 1 0 1 21 0 1 21 0 22 1 0 2 13 4 6 10 10 4 0 0 0 0

oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)
; dyads_m1 versus oligos_7nt_mkv2_m4; m=7/10; ncol2=24; w=0; offset=2; strand=D; shift=5; score=0.670121; -----yvsawmyatCGATAsTATCGAt ; cor=; Ncor= a 0 0 0 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 c 0 0 0 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 g 0 0 0 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 t 0 0 0 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; dyads_m1 versus oligos_7nt_mkv2_m2_rc; m=8/10; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.662242; wyhrTCGATASTATCGAyrktwby--- ; cor=; Ncor= a 6 3 5 9 2 1 2 16 0 18 1 2 17 1 0 1 14 1 5 3 4 5 2 2 0 0 0 c 4 8 7 2 1 15 0 1 1 0 13 0 1 1 19 0 1 5 4 2 3 1 6 8 0 0 0 g 4 3 2 5 2 1 17 1 1 1 5 0 0 0 0 18 3 2 8 7 1 2 6 3 0 0 0 t 5 5 5 3 14 2 0 1 17 0 0 17 1 17 0 0 1 11 2 7 11 11 5 6 0 0 0

dyads_m2_shift7 (dyads_m2)
; dyads_m1 versus dyads_m2; m=9/10; ncol2=24; w=0; offset=4; strand=D; shift=7; score=0.584379; -------saahbrTCGATAsTATCGAt ; cor=; Ncor= a 0 0 0 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 c 0 0 0 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 g 0 0 0 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 t 0 0 0 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10

positions_6nt_m1_shift11 (positions_6nt_m1)
; dyads_m1 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=8; strand=D; shift=11; score=0.415907; -----------haTCGATAGyw----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift3 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=24; shift=3; ncol=27; ---kyCGmTACwATCGATwGTAkCGrm ; Alignment reference a 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4

oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---kyCGmTACwATCGATwGTAkCGrm ; cor=; Ncor= a 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4

dyads_m1_shift3 (dyads_m1)
; oligos_6nt_mkv2_m1 versus dyads_m1; m=2/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---kyCGmTACwATCGATwGTAkCGrm ; cor=; Ncor= a 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4

oligos_7nt_mkv2_m1_shift3 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.991257; ---stCGmTActATCGATagTAkCGas ; cor=; Ncor= a 0 0 0 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 c 0 0 0 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 g 0 0 0 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 t 0 0 0 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3

oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=4/10; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.905742; ----tcGaTActATCGATAgTAtCGag ; cor=; Ncor= a 0 0 0 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 3 0 2 8 4 c 0 0 0 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 0 15 1 2 4 g 0 0 0 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 4 1 14 4 5 t 0 0 0 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4 10 1 0 3 4

dyads_m7_shift2 (dyads_m7)
; oligos_6nt_mkv2_m1 versus dyads_m7; m=5/10; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.864696; --wswCGATAsTATCGATwstwdYrw- ; cor=; Ncor= a 0 0 5 2 3 0 2 9 1 11 0 1 11 1 0 0 10 1 7 0 1 8 3 0 3 6 0 c 0 0 1 4 2 11 0 2 0 1 5 0 0 1 12 0 0 1 1 5 2 0 0 9 0 0 0 g 0 0 2 4 0 0 10 0 0 0 7 0 1 0 0 12 1 1 1 6 2 0 3 0 8 1 0 t 0 0 4 2 7 1 0 1 11 0 0 11 0 10 0 0 1 9 3 1 7 4 6 3 1 5 0

oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=6/10; ncol2=21; w=-1; offset=-1; strand=R; shift=2; score=0.681035; --daTCGATAsTATCGAtrkwws---- ; cor=; Ncor= a 0 0 6 11 2 0 1 21 0 22 1 2 21 1 0 1 16 3 7 5 6 6 5 0 0 0 0 c 0 0 5 3 2 21 0 1 0 0 14 0 2 0 22 0 1 5 4 4 3 3 7 0 0 0 0 g 0 0 6 5 3 1 22 0 2 1 7 0 0 0 0 22 4 2 8 8 4 4 7 0 0 0 0 t 0 0 6 4 16 1 0 1 21 0 1 21 0 22 1 0 2 13 4 6 10 10 4 0 0 0 0

oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=7/10; ncol2=24; w=0; offset=2; strand=D; shift=5; score=0.670121; -----yvsawmyatCGATAsTATCGAt ; cor=; Ncor= a 0 0 0 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 c 0 0 0 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 g 0 0 0 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 t 0 0 0 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13

oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=8/10; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.662242; wyhrTCGATASTATCGAyrktwby--- ; cor=; Ncor= a 6 3 5 9 2 1 2 16 0 18 1 2 17 1 0 1 14 1 5 3 4 5 2 2 0 0 0 c 4 8 7 2 1 15 0 1 1 0 13 0 1 1 19 0 1 5 4 2 3 1 6 8 0 0 0 g 4 3 2 5 2 1 17 1 1 1 5 0 0 0 0 18 3 2 8 7 1 2 6 3 0 0 0 t 5 5 5 3 14 2 0 1 17 0 0 17 1 17 0 0 1 11 2 7 11 11 5 6 0 0 0

dyads_m2_shift7 (dyads_m2)
; oligos_6nt_mkv2_m1 versus dyads_m2; m=9/10; ncol2=24; w=0; offset=4; strand=D; shift=7; score=0.584379; -------saahbrTCGATAsTATCGAt ; cor=; Ncor= a 0 0 0 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 c 0 0 0 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 g 0 0 0 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 t 0 0 0 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10

positions_6nt_m1_shift11 (positions_6nt_m1)
; oligos_6nt_mkv2_m1 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=8; strand=D; shift=11; score=0.415907; -----------haTCGATAGyw----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m10_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m10_shift2 (dyads_m10)
; dyads_m10; m=0 (reference); ncol1=10; shift=2; ncol=12; --ksCTGCACay ; Alignment reference a 0 0 2 2 0 0 0 0 22 0 11 3 c 0 0 3 6 22 0 2 21 0 22 3 7 g 0 0 10 11 0 0 20 1 0 0 4 4 t 0 0 7 3 0 22 0 0 0 0 4 8

dyads_m10_shift2 (dyads_m10)
; dyads_m10 versus dyads_m10; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --ksCTGCACay ; cor=; Ncor= a 0 0 2 2 0 0 0 0 22 0 11 3 c 0 0 3 6 22 0 2 21 0 22 3 7 g 0 0 10 11 0 0 20 1 0 0 4 4 t 0 0 7 3 0 22 0 0 0 0 4 8

dyads_m8_rc_shift0 (dyads_m8_rc)
; dyads_m10 versus dyads_m8_rc; m=2/2; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.496458; scTGCTGCws-- ; cor=; Ncor= a 6 4 0 0 0 0 0 0 11 6 0 0 c 10 13 0 0 30 0 0 30 7 9 0 0 g 10 6 0 30 0 0 30 0 4 11 0 0 t 4 7 30 0 0 30 0 0 8 4 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=2; ncol=12; --rwAAAATAww ; Alignment reference a 0 0 12 13 35 35 35 35 0 35 10 10 c 0 0 5 6 0 0 0 0 0 0 8 8 g 0 0 10 6 0 0 0 0 0 0 4 7 t 0 0 8 10 0 0 0 0 35 0 13 10

oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --rwAAAATAww ; cor=; Ncor= a 0 0 12 13 35 35 35 35 0 35 10 10 c 0 0 5 6 0 0 0 0 0 0 8 8 g 0 0 10 6 0 0 0 0 0 0 4 7 t 0 0 8 10 0 0 0 0 35 0 13 10

dyads_m3_shift1 (dyads_m3)
; oligos_6nt_mkv2_m3 versus dyads_m3; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score= 0.9071; -wrwAAAATAww ; cor=; Ncor= a 0 14 13 13 38 38 35 38 0 38 11 11 c 0 8 7 6 0 0 0 0 0 0 9 8 g 0 1 10 6 0 0 0 0 0 0 5 8 t 0 15 8 13 0 0 3 0 38 0 13 11

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=3/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.631862; twaATAAATAww ; cor=; Ncor= a 8 14 24 40 3 37 35 40 2 38 13 11 c 7 10 3 1 2 1 0 0 1 1 9 8 g 6 4 4 0 4 1 2 1 0 1 5 10 t 20 13 10 0 32 2 4 0 38 1 14 12

One-to-n matrix alignment; reference matrix: dyads_m7_shift3 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift3 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=24; shift=3; ncol=27; ---wswCGATAsTATCGATwstwdYrw ; Alignment reference a 0 0 0 5 2 3 0 2 9 1 11 0 1 11 1 0 0 10 1 7 0 1 8 3 0 3 6 c 0 0 0 1 4 2 11 0 2 0 1 5 0 0 1 12 0 0 1 1 5 2 0 0 9 0 0 g 0 0 0 2 4 0 0 10 0 0 0 7 0 1 0 0 12 1 1 1 6 2 0 3 0 8 1 t 0 0 0 4 2 7 1 0 1 11 0 0 11 0 10 0 0 1 9 3 1 7 4 6 3 1 5

dyads_m7_shift3 (dyads_m7)
; dyads_m7 versus dyads_m7; m=1/9; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---wswCGATAsTATCGATwstwdYrw ; cor=; Ncor= a 0 0 0 5 2 3 0 2 9 1 11 0 1 11 1 0 0 10 1 7 0 1 8 3 0 3 6 c 0 0 0 1 4 2 11 0 2 0 1 5 0 0 1 12 0 0 1 1 5 2 0 0 9 0 0 g 0 0 0 2 4 0 0 10 0 0 0 7 0 1 0 0 12 1 1 1 6 2 0 3 0 8 1 t 0 0 0 4 2 7 1 0 1 11 0 0 11 0 10 0 0 1 9 3 1 7 4 6 3 1 5

oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)
; dyads_m7 versus oligos_7nt_mkv2_m5; m=2/9; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.950765; ---actCGaTAcTATCGATagTAtCga ; cor=; Ncor= a 0 0 0 6 4 3 0 1 10 4 14 2 2 15 1 0 1 15 0 11 1 2 12 4 0 2 10 c 0 0 0 4 5 4 14 1 4 0 1 11 3 1 1 16 0 0 1 0 4 1 1 0 12 4 1 g 0 0 0 3 4 2 1 15 0 1 1 4 0 1 0 0 16 1 1 2 10 2 0 4 2 11 3 t 0 0 0 4 4 8 2 0 3 12 1 0 12 0 15 1 0 1 15 4 2 12 4 9 3 0 3

oligos_7nt_mkv2_m1_shift4 (oligos_7nt_mkv2_m1)
; dyads_m7 versus oligos_7nt_mkv2_m1; m=3/9; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.866355; ----stCGmTActATCGATagTAkCGa ; cor=; Ncor= a 0 0 0 0 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 c 0 0 0 0 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 g 0 0 0 0 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 t 0 0 0 0 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3

dyads_m1_shift4 (dyads_m1)
; dyads_m7 versus dyads_m1; m=4/9; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.864696; ----kyCGmTACwATCGATwGTAkCGr ; cor=; Ncor= a 0 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 c 0 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 g 0 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 t 0 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4

oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)
; dyads_m7 versus oligos_6nt_mkv2_m1; m=5/9; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.864696; ----kyCGmTACwATCGATwGTAkCGr ; cor=; Ncor= a 0 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 c 0 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 g 0 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 t 0 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4

oligos_7nt_mkv2_m4_rc_shift2 (oligos_7nt_mkv2_m4_rc)
; dyads_m7 versus oligos_7nt_mkv2_m4_rc; m=6/9; ncol2=24; w=-1; offset=-1; strand=R; shift=2; score=0.796152; --cwaTCGATAsTATCGatrkwtsbr- ; cor=; Ncor= a 0 0 3 6 13 2 1 2 20 0 21 1 1 21 1 0 0 15 2 6 4 6 3 4 3 8 0 c 0 0 12 5 3 2 20 0 0 2 0 15 0 1 1 22 0 1 5 4 4 3 3 8 8 4 0 g 0 0 3 5 5 2 1 21 2 1 1 7 0 0 0 0 23 5 4 9 8 4 4 7 6 7 0 t 0 0 5 7 2 17 1 0 1 20 1 0 22 1 21 1 0 2 12 4 7 10 13 4 6 4 0

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)
; dyads_m7 versus oligos_6nt_mkv2_m2_rc; m=7/9; ncol2=21; w=0; offset=0; strand=R; shift=3; score=0.794986; ---daTCGATAsTATCGAtrkwws--- ; cor=; Ncor= a 0 0 0 6 11 2 0 1 21 0 22 1 2 21 1 0 1 16 3 7 5 6 6 5 0 0 0 c 0 0 0 5 3 2 21 0 1 0 0 14 0 2 0 22 0 1 5 4 4 3 3 7 0 0 0 g 0 0 0 6 5 3 1 22 0 2 1 7 0 0 0 0 22 4 2 8 8 4 4 7 0 0 0 t 0 0 0 6 4 16 1 0 1 21 0 1 21 0 22 1 0 2 13 4 6 10 10 4 0 0 0

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)
; dyads_m7 versus oligos_7nt_mkv2_m2_rc; m=8/9; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.753248; -wyhrTCGATASTATCGAyrktwby-- ; cor=; Ncor= a 0 6 3 5 9 2 1 2 16 0 18 1 2 17 1 0 1 14 1 5 3 4 5 2 2 0 0 c 0 4 8 7 2 1 15 0 1 1 0 13 0 1 1 19 0 1 5 4 2 3 1 6 8 0 0 g 0 4 3 2 5 2 1 17 1 1 1 5 0 0 0 0 18 3 2 8 7 1 2 6 3 0 0 t 0 5 5 5 3 14 2 0 1 17 0 0 17 1 17 0 0 1 11 2 7 11 11 5 6 0 0

dyads_m2_rc_shift0 (dyads_m2_rc)
; dyads_m7 versus dyads_m2_rc; m=9/9; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.680859; ayhyaTCGATAsTATCGAyvdtts--- ; cor=; Ncor= a 8 3 4 3 10 0 1 1 15 0 16 0 1 13 1 0 1 12 1 4 4 3 3 2 0 0 0 c 2 4 6 5 0 1 15 0 0 0 0 10 0 2 1 16 0 1 4 4 1 3 3 5 0 0 0 g 3 3 2 3 3 2 0 15 0 1 0 6 0 0 0 0 15 2 2 6 6 3 2 6 0 0 0 t 3 6 4 5 3 13 0 0 1 15 0 0 15 1 14 0 0 1 9 2 5 7 8 3 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift0 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; aaACATCGrtk ; Alignment reference a 25 23 41 1 46 1 1 1 16 11 10 c 7 10 6 45 1 0 47 2 3 11 6 g 8 7 2 1 1 1 1 45 29 8 14 t 9 9 0 2 1 47 0 1 1 19 19

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; aaACATCGrtk ; cor=; Ncor= a 25 23 41 1 46 1 1 1 16 11 10 c 7 10 6 45 1 0 47 2 3 11 6 g 8 7 2 1 1 1 1 45 29 8 14 t 9 9 0 2 1 47 0 1 1 19 19

One-to-n matrix alignment; reference matrix: dyads_m3_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift1 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wrwAAAATAww ; Alignment reference a 0 14 13 13 38 38 35 38 0 38 11 11 c 0 8 7 6 0 0 0 0 0 0 9 8 g 0 1 10 6 0 0 0 0 0 0 5 8 t 0 15 8 13 0 0 3 0 38 0 13 11

dyads_m3_shift1 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wrwAAAATAww ; cor=; Ncor= a 0 14 13 13 38 38 35 38 0 38 11 11 c 0 8 7 6 0 0 0 0 0 0 9 8 g 0 1 10 6 0 0 0 0 0 0 5 8 t 0 15 8 13 0 0 3 0 38 0 13 11

oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)
; dyads_m3 versus oligos_6nt_mkv2_m3; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=2; score= 0.9071; --rwAAAATAww ; cor=; Ncor= a 0 0 12 13 35 35 35 35 0 35 10 10 c 0 0 5 6 0 0 0 0 0 0 8 8 g 0 0 10 6 0 0 0 0 0 0 4 7 t 0 0 8 10 0 0 0 0 35 0 13 10

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; dyads_m3 versus oligos_7nt_mkv2_m3; m=3/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.688871; twaATAAATAww ; cor=; Ncor= a 8 14 24 40 3 37 35 40 2 38 13 11 c 7 10 3 1 2 1 0 0 1 1 9 8 g 6 4 4 0 4 1 2 1 0 1 5 10 t 20 13 10 0 32 2 4 0 38 1 14 12

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift4 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=21; shift=4; ncol=25; ----swwmyaTCGATAsTATCGAth ; Alignment reference a 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 6 c 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 6 g 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 5 t 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11 6

oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/10; ncol2=21; w=0; offset=0; strand=D; shift=4; score= 1; ----swwmyaTCGATAsTATCGAth ; cor=; Ncor= a 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 6 c 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 6 g 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 5 t 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11 6

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=2/10; ncol2=24; w=-2; offset=-2; strand=D; shift=2; score=0.866938; --yvsawmyatCGATAsTATCGAtw ; cor=; Ncor= a 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 7 c 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 5 g 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 5 t 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13 6

dyads_m2_shift4 (dyads_m2)
; oligos_6nt_mkv2_m2 versus dyads_m2; m=3/10; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.862825; ----saahbrTCGATAsTATCGAtr ; cor=; Ncor= a 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 5 c 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 3 g 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 5 t 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10 3

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=4/10; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.859793; ---rvwamyrTCGATASTATCGAyd ; cor=; Ncor= a 0 0 0 6 5 11 11 7 2 11 1 0 0 17 1 17 0 0 17 1 0 2 14 3 5 c 0 0 0 3 6 2 1 7 8 2 3 18 0 0 0 0 5 1 1 1 17 1 2 5 2 g 0 0 0 8 6 1 3 2 4 5 1 0 19 1 1 0 13 0 1 1 0 15 1 2 7 t 0 0 0 2 2 5 4 3 5 1 14 1 0 1 17 2 1 18 0 16 2 1 2 9 5

dyads_m7_rc_shift1 (dyads_m7_rc)
; oligos_6nt_mkv2_m2 versus dyads_m7_rc; m=5/10; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.794986; -wyRhwaswATCGATAsTATCGwsw ; cor=; Ncor= a 0 5 1 3 6 4 7 1 3 9 1 0 0 10 0 11 0 0 11 1 0 1 7 2 4 c 0 1 8 0 3 0 2 6 1 1 1 12 0 0 1 0 7 0 0 0 10 0 0 4 2 g 0 0 0 9 0 0 2 5 1 1 0 0 12 1 0 0 5 1 0 2 0 11 2 4 1 t 0 6 3 0 3 8 1 0 7 1 10 0 0 1 11 1 0 11 1 9 2 0 3 2 5

oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m5_rc; m=6/10; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.772413; -tcGaTActATCGATAgTAtCGagt ; cor=; Ncor= a 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 3 0 2 8 4 4 c 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 0 15 1 2 4 3 g 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 4 1 14 4 5 4 t 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4 10 1 0 3 4 6

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=7/10; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.688257; stCGmTActATCGATagTAkCGas- ; cor=; Ncor= a 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 0 c 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 0 g 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 0 t 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3 0

dyads_m1_shift0 (dyads_m1)
; oligos_6nt_mkv2_m2 versus dyads_m1; m=8/10; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.681035; kyCGmTACwATCGATwGTAkCGrm- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=9/10; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.681035; kyCGmTACwATCGATwGTAkCGrm- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0

positions_6nt_m1_shift8 (positions_6nt_m1)
; oligos_6nt_mkv2_m2 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=4; strand=D; shift=8; score=0.471129; --------haTCGATAGyw------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m2_shift4 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift4 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=24; shift=4; ncol=28; ----saahbrTCGATAsTATCGAtrdrt ; Alignment reference a 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 5 4 6 3 c 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 3 2 3 3 g 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 5 6 4 2 t 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10 3 4 3 8

dyads_m2_shift4 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----saahbrTCGATAsTATCGAtrdrt ; cor=; Ncor= a 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 5 4 6 3 c 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 3 2 3 3 g 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 5 6 4 2 t 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10 3 4 3 8

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; dyads_m2 versus oligos_7nt_mkv2_m2; m=2/10; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.90157; ---rvwamyrTCGATASTATCGAydrw- ; cor=; Ncor= a 0 0 0 6 5 11 11 7 2 11 1 0 0 17 1 17 0 0 17 1 0 2 14 3 5 5 5 0 c 0 0 0 3 6 2 1 7 8 2 3 18 0 0 0 0 5 1 1 1 17 1 2 5 2 3 4 0 g 0 0 0 8 6 1 3 2 4 5 1 0 19 1 1 0 13 0 1 1 0 15 1 2 7 8 4 0 t 0 0 0 2 2 5 4 3 5 1 14 1 0 1 17 2 1 18 0 16 2 1 2 9 5 3 6 0

oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)
; dyads_m2 versus oligos_6nt_mkv2_m2; m=3/10; ncol2=21; w=0; offset=0; strand=D; shift=4; score=0.862825; ----swwmyaTCGATAsTATCGAth--- ; cor=; Ncor= a 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 6 0 0 0 c 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 6 0 0 0 g 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 5 0 0 0 t 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11 6 0 0 0

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; dyads_m2 versus oligos_7nt_mkv2_m4; m=4/10; ncol2=24; w=-2; offset=-2; strand=D; shift=2; score=0.831938; --yvsawmyatCGATAsTATCGAtwg-- ; cor=; Ncor= a 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 7 5 0 0 c 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 5 3 0 0 g 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 5 12 0 0 t 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13 6 3 0 0

dyads_m7_rc_shift1 (dyads_m7_rc)
; dyads_m2 versus dyads_m7_rc; m=5/10; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.680859; -wyRhwaswATCGATAsTATCGwsw--- ; cor=; Ncor= a 0 5 1 3 6 4 7 1 3 9 1 0 0 10 0 11 0 0 11 1 0 1 7 2 4 0 0 0 c 0 1 8 0 3 0 2 6 1 1 1 12 0 0 1 0 7 0 0 0 10 0 0 4 2 0 0 0 g 0 0 0 9 0 0 2 5 1 1 0 0 12 1 0 0 5 1 0 2 0 11 2 4 1 0 0 0 t 0 6 3 0 3 8 1 0 7 1 10 0 0 1 11 1 0 11 1 9 2 0 3 2 5 0 0 0

oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)
; dyads_m2 versus oligos_7nt_mkv2_m5_rc; m=6/10; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.65843; -tcGaTActATCGATAgTAtCGagt--- ; cor=; Ncor= a 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 3 0 2 8 4 4 0 0 0 c 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 0 15 1 2 4 3 0 0 0 g 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 4 1 14 4 5 4 0 0 0 t 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4 10 1 0 3 4 6 0 0 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; dyads_m2 versus oligos_7nt_mkv2_m1; m=7/10; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.590481; stCGmTActATCGATagTAkCGas---- ; cor=; Ncor= a 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 0 0 0 0 c 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 0 0 0 0 g 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 0 0 0 0 t 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3 0 0 0 0

dyads_m1_shift0 (dyads_m1)
; dyads_m2 versus dyads_m1; m=8/10; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.584379; kyCGmTACwATCGATwGTAkCGrm---- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 0 0 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 0 0 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 0 0 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0 0 0 0

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; dyads_m2 versus oligos_6nt_mkv2_m1; m=9/10; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.584379; kyCGmTACwATCGATwGTAkCGrm---- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 0 0 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 0 0 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 0 0 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0 0 0 0

positions_6nt_m1_shift8 (positions_6nt_m1)
; dyads_m2 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=4; strand=D; shift=8; score=0.403924; --------haTCGATAGyw--------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift8 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift8 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=11; shift=8; ncol=19; --------haTCGATAGyw ; Alignment reference a 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 c 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 g 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 t 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28

positions_6nt_m1_shift8 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/9; ncol2=11; w=0; offset=0; strand=D; shift=8; score= 1; --------haTCGATAGyw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 c 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 g 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 t 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28

oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)
; positions_6nt_m1 versus oligos_6nt_mkv2_m2; m=2/9; ncol2=21; w=-4; offset=-4; strand=D; shift=4; score=0.471129; ----swwmyaTCGATAsTA ; cor=; Ncor= a 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 c 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 g 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 t 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0

oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)
; positions_6nt_m1 versus oligos_7nt_mkv2_m5_rc; m=3/9; ncol2=24; w=-7; offset=-7; strand=R; shift=1; score=0.41645; -tcGaTActATCGATAgTA ; cor=; Ncor= a 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 c 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 g 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 t 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; positions_6nt_m1 versus oligos_7nt_mkv2_m1; m=4/9; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.41602; stCGmTActATCGATagTA ; cor=; Ncor= a 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 c 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 g 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 t 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; positions_6nt_m1 versus oligos_6nt_mkv2_m1; m=5/9; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.415907; kyCGmTACwATCGATwGTA ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5

dyads_m1_shift0 (dyads_m1)
; positions_6nt_m1 versus dyads_m1; m=6/9; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.415907; kyCGmTACwATCGATwGTA ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; positions_6nt_m1 versus oligos_7nt_mkv2_m4; m=7/9; ncol2=24; w=-6; offset=-6; strand=D; shift=2; score=0.415068; --yvsawmyatCGATAsTA ; cor=; Ncor= a 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 c 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 g 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 t 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; positions_6nt_m1 versus oligos_7nt_mkv2_m2; m=8/9; ncol2=24; w=-5; offset=-5; strand=D; shift=3; score=0.413795; ---rvwamyrTCGATASTA ; cor=; Ncor= a 0 0 0 6 5 11 11 7 2 11 1 0 0 17 1 17 0 0 17 c 0 0 0 3 6 2 1 7 8 2 3 18 0 0 0 0 5 1 1 g 0 0 0 8 6 1 3 2 4 5 1 0 19 1 1 0 13 0 1 t 0 0 0 2 2 5 4 3 5 1 14 1 0 1 17 2 1 18 0

dyads_m2_shift4 (dyads_m2)
; positions_6nt_m1 versus dyads_m2; m=9/9; ncol2=24; w=-4; offset=-4; strand=D; shift=4; score=0.403924; ----saahbrTCGATAsTA ; cor=; Ncor= a 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 c 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 g 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 t 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift3 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=24; shift=3; ncol=27; ---actCGaTAcTATCGATagTAtCga ; Alignment reference a 0 0 0 6 4 3 0 1 10 4 14 2 2 15 1 0 1 15 0 11 1 2 12 4 0 2 10 c 0 0 0 4 5 4 14 1 4 0 1 11 3 1 1 16 0 0 1 0 4 1 1 0 12 4 1 g 0 0 0 3 4 2 1 15 0 1 1 4 0 1 0 0 16 1 1 2 10 2 0 4 2 11 3 t 0 0 0 4 4 8 2 0 3 12 1 0 12 0 15 1 0 1 15 4 2 12 4 9 3 0 3

oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---actCGaTAcTATCGATagTAtCga ; cor=; Ncor= a 0 0 0 6 4 3 0 1 10 4 14 2 2 15 1 0 1 15 0 11 1 2 12 4 0 2 10 c 0 0 0 4 5 4 14 1 4 0 1 11 3 1 1 16 0 0 1 0 4 1 1 0 12 4 1 g 0 0 0 3 4 2 1 15 0 1 1 4 0 1 0 0 16 1 1 2 10 2 0 4 2 11 3 t 0 0 0 4 4 8 2 0 3 12 1 0 12 0 15 1 0 1 15 4 2 12 4 9 3 0 3

dyads_m7_shift3 (dyads_m7)
; oligos_7nt_mkv2_m5 versus dyads_m7; m=2/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.950765; ---wswCGATAsTATCGATwstwdYrw ; cor=; Ncor= a 0 0 0 5 2 3 0 2 9 1 11 0 1 11 1 0 0 10 1 7 0 1 8 3 0 3 6 c 0 0 0 1 4 2 11 0 2 0 1 5 0 0 1 12 0 0 1 1 5 2 0 0 9 0 0 g 0 0 0 2 4 0 0 10 0 0 0 7 0 1 0 0 12 1 1 1 6 2 0 3 0 8 1 t 0 0 0 4 2 7 1 0 1 11 0 0 11 0 10 0 0 1 9 3 1 7 4 6 3 1 5

oligos_7nt_mkv2_m1_shift4 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=3/10; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.911191; ----stCGmTActATCGATagTAkCGa ; cor=; Ncor= a 0 0 0 0 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 c 0 0 0 0 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 g 0 0 0 0 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 t 0 0 0 0 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3

oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=4/10; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.905742; ----kyCGmTACwATCGATwGTAkCGr ; cor=; Ncor= a 0 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 c 0 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 g 0 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 t 0 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4

dyads_m1_shift4 (dyads_m1)
; oligos_7nt_mkv2_m5 versus dyads_m1; m=5/10; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.905742; ----kyCGmTACwATCGATwGTAkCGr ; cor=; Ncor= a 0 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 c 0 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 g 0 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 t 0 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4

oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m2_rc; m=6/10; ncol2=21; w=0; offset=0; strand=R; shift=3; score=0.772413; ---daTCGATAsTATCGAtrkwws--- ; cor=; Ncor= a 0 0 0 6 11 2 0 1 21 0 22 1 2 21 1 0 1 16 3 7 5 6 6 5 0 0 0 c 0 0 0 5 3 2 21 0 1 0 0 14 0 2 0 22 0 1 5 4 4 3 3 7 0 0 0 g 0 0 0 6 5 3 1 22 0 2 1 7 0 0 0 0 22 4 2 8 8 4 4 7 0 0 0 t 0 0 0 6 4 16 1 0 1 21 0 1 21 0 22 1 0 2 13 4 6 10 10 4 0 0 0

oligos_7nt_mkv2_m4_rc_shift2 (oligos_7nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m4_rc; m=7/10; ncol2=24; w=-1; offset=-1; strand=R; shift=2; score=0.765826; --cwaTCGATAsTATCGatrkwtsbr- ; cor=; Ncor= a 0 0 3 6 13 2 1 2 20 0 21 1 1 21 1 0 0 15 2 6 4 6 3 4 3 8 0 c 0 0 12 5 3 2 20 0 0 2 0 15 0 1 1 22 0 1 5 4 4 3 3 8 8 4 0 g 0 0 3 5 5 2 1 21 2 1 1 7 0 0 0 0 23 5 4 9 8 4 4 7 6 7 0 t 0 0 5 7 2 17 1 0 1 20 1 0 22 1 21 1 0 2 12 4 7 10 13 4 6 4 0

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2_rc; m=8/10; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.740443; -wyhrTCGATASTATCGAyrktwby-- ; cor=; Ncor= a 0 6 3 5 9 2 1 2 16 0 18 1 2 17 1 0 1 14 1 5 3 4 5 2 2 0 0 c 0 4 8 7 2 1 15 0 1 1 0 13 0 1 1 19 0 1 5 4 2 3 1 6 8 0 0 g 0 4 3 2 5 2 1 17 1 1 1 5 0 0 0 0 18 3 2 8 7 1 2 6 3 0 0 t 0 5 5 5 3 14 2 0 1 17 0 0 17 1 17 0 0 1 11 2 7 11 11 5 6 0 0

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv2_m5 versus dyads_m2_rc; m=9/10; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.65843; ayhyaTCGATAsTATCGAyvdtts--- ; cor=; Ncor= a 8 3 4 3 10 0 1 1 15 0 16 0 1 13 1 0 1 12 1 4 4 3 3 2 0 0 0 c 2 4 6 5 0 1 15 0 0 0 0 10 0 2 1 16 0 1 4 4 1 3 3 5 0 0 0 g 3 3 2 3 3 2 0 15 0 1 0 6 0 0 0 0 15 2 2 6 6 3 2 6 0 0 0 t 3 6 4 5 3 13 0 0 1 15 0 0 15 1 14 0 0 1 9 2 5 7 8 3 0 0 0

positions_6nt_m1_rc_shift9 (positions_6nt_m1_rc)
; oligos_7nt_mkv2_m5 versus positions_6nt_m1_rc; m=10/10; ncol2=11; w=0; offset=6; strand=R; shift=9; score=0.41645; ---------wrCTATCGAtd------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 28 38 4 6 79 1 1 1 74 16 25 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 14 12 69 8 3 0 86 1 4 16 14 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 15 27 12 0 2 2 1 84 5 11 24 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 31 11 3 74 4 85 0 2 5 45 25 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift2 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=24; shift=2; ncol=26; --yvsawmyatCGATAsTATCGAtwg ; Alignment reference a 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 7 5 c 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 5 3 g 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 5 12 t 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13 6 3

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --yvsawmyatCGATAsTATCGAtwg ; cor=; Ncor= a 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 7 5 c 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 5 3 g 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 5 12 t 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13 6 3

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=2/10; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.904547; ---rvwamyrTCGATASTATCGAydr ; cor=; Ncor= a 0 0 0 6 5 11 11 7 2 11 1 0 0 17 1 17 0 0 17 1 0 2 14 3 5 5 c 0 0 0 3 6 2 1 7 8 2 3 18 0 0 0 0 5 1 1 1 17 1 2 5 2 3 g 0 0 0 8 6 1 3 2 4 5 1 0 19 1 1 0 13 0 1 1 0 15 1 2 7 8 t 0 0 0 2 2 5 4 3 5 1 14 1 0 1 17 2 1 18 0 16 2 1 2 9 5 3

oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=3/10; ncol2=21; w=0; offset=2; strand=D; shift=4; score=0.866938; ----swwmyaTCGATAsTATCGAth- ; cor=; Ncor= a 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 6 0 c 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 6 0 g 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 5 0 t 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11 6 0

dyads_m2_shift4 (dyads_m2)
; oligos_7nt_mkv2_m4 versus dyads_m2; m=4/10; ncol2=24; w=0; offset=2; strand=D; shift=4; score=0.831938; ----saahbrTCGATAsTATCGAtrd ; cor=; Ncor= a 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 5 4 c 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 3 2 g 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 5 6 t 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10 3 4

dyads_m7_rc_shift1 (dyads_m7_rc)
; oligos_7nt_mkv2_m4 versus dyads_m7_rc; m=5/10; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.796152; -wyRhwaswATCGATAsTATCGwsw- ; cor=; Ncor= a 0 5 1 3 6 4 7 1 3 9 1 0 0 10 0 11 0 0 11 1 0 1 7 2 4 0 c 0 1 8 0 3 0 2 6 1 1 1 12 0 0 1 0 7 0 0 0 10 0 0 4 2 0 g 0 0 0 9 0 0 2 5 1 1 0 0 12 1 0 0 5 1 0 2 0 11 2 4 1 0 t 0 6 3 0 3 8 1 0 7 1 10 0 0 1 11 1 0 11 1 9 2 0 3 2 5 0

oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m5_rc; m=6/10; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.765826; -tcGaTActATCGATAgTAtCGagt- ; cor=; Ncor= a 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 3 0 2 8 4 4 0 c 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 0 15 1 2 4 3 0 g 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 4 1 14 4 5 4 0 t 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4 10 1 0 3 4 6 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=7/10; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.680504; stCGmTActATCGATagTAkCGas-- ; cor=; Ncor= a 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 0 0 c 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 0 0 g 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 0 0 t 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3 0 0

dyads_m1_shift0 (dyads_m1)
; oligos_7nt_mkv2_m4 versus dyads_m1; m=8/10; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.670121; kyCGmTACwATCGATwGTAkCGrm-- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0 0

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=9/10; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.670121; kyCGmTACwATCGATwGTAkCGrm-- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0 0

positions_6nt_m1_shift8 (positions_6nt_m1)
; oligos_7nt_mkv2_m4 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=6; strand=D; shift=8; score=0.415068; --------haTCGATAGyw------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift0 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=14; shift=0; ncol=14; hcCCCamcyCCCmr ; Alignment reference a 11 9 3 2 1 24 11 10 6 2 2 7 13 11 c 12 14 35 38 36 8 15 16 15 38 36 34 12 10 g 6 10 0 0 2 3 5 10 9 0 0 0 6 11 t 12 8 3 1 2 6 10 5 11 1 3 0 10 9

dyads_m6_shift0 (dyads_m6)
; dyads_m6 versus dyads_m6; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; hcCCCamcyCCCmr ; cor=; Ncor= a 11 9 3 2 1 24 11 10 6 2 2 7 13 11 c 12 14 35 38 36 8 15 16 15 38 36 34 12 10 g 6 10 0 0 2 3 5 10 9 0 0 0 6 11 t 12 8 3 1 2 6 10 5 11 1 3 0 10 9

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; twaATAAATAww ; Alignment reference a 8 14 24 40 3 37 35 40 2 38 13 11 c 7 10 3 1 2 1 0 0 1 1 9 8 g 6 4 4 0 4 1 2 1 0 1 5 10 t 20 13 10 0 32 2 4 0 38 1 14 12

oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; twaATAAATAww ; cor=; Ncor= a 8 14 24 40 3 37 35 40 2 38 13 11 c 7 10 3 1 2 1 0 0 1 1 9 8 g 6 4 4 0 4 1 2 1 0 1 5 10 t 20 13 10 0 32 2 4 0 38 1 14 12

dyads_m3_shift1 (dyads_m3)
; oligos_7nt_mkv2_m3 versus dyads_m3; m=2/3; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.688871; -wrwAAAATAww ; cor=; Ncor= a 0 14 13 13 38 38 35 38 0 38 11 11 c 0 8 7 6 0 0 0 0 0 0 9 8 g 0 1 10 6 0 0 0 0 0 0 5 8 t 0 15 8 13 0 0 3 0 38 0 13 11

oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.631862; --rwAAAATAww ; cor=; Ncor= a 0 0 12 13 35 35 35 35 0 35 10 10 c 0 0 5 6 0 0 0 0 0 0 8 8 g 0 0 10 6 0 0 0 0 0 0 4 7 t 0 0 8 10 0 0 0 0 35 0 13 10

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift4 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift4 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=24; shift=4; ncol=28; ----stCGmTActATCGATagTAkCGas ; Alignment reference a 0 0 0 0 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 c 0 0 0 0 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 g 0 0 0 0 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 t 0 0 0 0 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3

oligos_7nt_mkv2_m1_shift4 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----stCGmTActATCGATagTAkCGas ; cor=; Ncor= a 0 0 0 0 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 c 0 0 0 0 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 g 0 0 0 0 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 t 0 0 0 0 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3

oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/10; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.991257; ----kyCGmTACwATCGATwGTAkCGrm ; cor=; Ncor= a 0 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4

dyads_m1_shift4 (dyads_m1)
; oligos_7nt_mkv2_m1 versus dyads_m1; m=3/10; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.991257; ----kyCGmTACwATCGATwGTAkCGrm ; cor=; Ncor= a 0 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4

oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=4/10; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.911191; ---actCGaTAcTATCGATagTAtCga- ; cor=; Ncor= a 0 0 0 6 4 3 0 1 10 4 14 2 2 15 1 0 1 15 0 11 1 2 12 4 0 2 10 0 c 0 0 0 4 5 4 14 1 4 0 1 11 3 1 1 16 0 0 1 0 4 1 1 0 12 4 1 0 g 0 0 0 3 4 2 1 15 0 1 1 4 0 1 0 0 16 1 1 2 10 2 0 4 2 11 3 0 t 0 0 0 4 4 8 2 0 3 12 1 0 12 0 15 1 0 1 15 4 2 12 4 9 3 0 3 0

dyads_m7_shift3 (dyads_m7)
; oligos_7nt_mkv2_m1 versus dyads_m7; m=5/10; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.866355; ---wswCGATAsTATCGATwstwdYrw- ; cor=; Ncor= a 0 0 0 5 2 3 0 2 9 1 11 0 1 11 1 0 0 10 1 7 0 1 8 3 0 3 6 0 c 0 0 0 1 4 2 11 0 2 0 1 5 0 0 1 12 0 0 1 1 5 2 0 0 9 0 0 0 g 0 0 0 2 4 0 0 10 0 0 0 7 0 1 0 0 12 1 1 1 6 2 0 3 0 8 1 0 t 0 0 0 4 2 7 1 0 1 11 0 0 11 0 10 0 0 1 9 3 1 7 4 6 3 1 5 0

oligos_6nt_mkv2_m2_shift8 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=6/10; ncol2=21; w=0; offset=4; strand=D; shift=8; score=0.688257; --------swwmyaTCGATAsTATCGAt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 c 0 0 0 0 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 g 0 0 0 0 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 t 0 0 0 0 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11

oligos_7nt_mkv2_m4_shift6 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=7/10; ncol2=24; w=0; offset=2; strand=D; shift=6; score=0.680504; ------yvsawmyatCGATAsTATCGAt ; cor=; Ncor= a 0 0 0 0 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 c 0 0 0 0 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 g 0 0 0 0 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 t 0 0 0 0 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13

oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=8/10; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.668967; -wyhrTCGATASTATCGAyrktwby--- ; cor=; Ncor= a 0 6 3 5 9 2 1 2 16 0 18 1 2 17 1 0 1 14 1 5 3 4 5 2 2 0 0 0 c 0 4 8 7 2 1 15 0 1 1 0 13 0 1 1 19 0 1 5 4 2 3 1 6 8 0 0 0 g 0 4 3 2 5 2 1 17 1 1 1 5 0 0 0 0 18 3 2 8 7 1 2 6 3 0 0 0 t 0 5 5 5 3 14 2 0 1 17 0 0 17 1 17 0 0 1 11 2 7 11 11 5 6 0 0 0

dyads_m2_rc_shift0 (dyads_m2_rc)
; oligos_7nt_mkv2_m1 versus dyads_m2_rc; m=9/10; ncol2=24; w=-4; offset=-4; strand=R; shift=0; score=0.590481; ayhyaTCGATAsTATCGAyvdtts---- ; cor=; Ncor= a 8 3 4 3 10 0 1 1 15 0 16 0 1 13 1 0 1 12 1 4 4 3 3 2 0 0 0 0 c 2 4 6 5 0 1 15 0 0 0 0 10 0 2 1 16 0 1 4 4 1 3 3 5 0 0 0 0 g 3 3 2 3 3 2 0 15 0 1 0 6 0 0 0 0 15 2 2 6 6 3 2 6 0 0 0 0 t 3 6 4 5 3 13 0 0 1 15 0 0 15 1 14 0 0 1 9 2 5 7 8 3 0 0 0 0

positions_6nt_m1_shift12 (positions_6nt_m1)
; oligos_7nt_mkv2_m1 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=8; strand=D; shift=12; score=0.41602; ------------haTCGATAGyw----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m8_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m8_shift2 (dyads_m8)
; dyads_m8; m=0 (reference); ncol1=10; shift=2; ncol=12; --swGCAGCAgs ; Alignment reference a 0 0 4 8 0 0 30 0 0 30 7 4 c 0 0 11 4 0 30 0 0 30 0 6 10 g 0 0 9 7 30 0 0 30 0 0 13 10 t 0 0 6 11 0 0 0 0 0 0 4 6

dyads_m8_shift2 (dyads_m8)
; dyads_m8 versus dyads_m8; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --swGCAGCAgs ; cor=; Ncor= a 0 0 4 8 0 0 30 0 0 30 7 4 c 0 0 11 4 0 30 0 0 30 0 6 10 g 0 0 9 7 30 0 0 30 0 0 13 10 t 0 0 6 11 0 0 0 0 0 0 4 6

dyads_m10_rc_shift0 (dyads_m10_rc)
; dyads_m8 versus dyads_m10_rc; m=2/2; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.496458; rtGTGCAGsm-- ; cor=; Ncor= a 8 4 0 0 0 0 22 0 3 7 0 0 c 4 4 0 0 1 20 0 0 11 10 0 0 g 7 3 22 0 21 2 0 22 6 3 0 0 t 3 11 0 22 0 0 0 0 2 2 0 0

One-to-n matrix alignment; reference matrix: dyads_m9_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift0 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=16; shift=0; ncol=16; wwTAAwrhwymAAAaw ; Alignment reference a 11 9 0 23 23 9 9 6 9 4 8 22 23 23 11 9 c 3 5 0 0 0 1 1 8 2 7 6 0 0 0 3 5 g 2 2 0 0 0 4 8 3 5 5 5 0 0 0 4 2 t 7 7 23 0 0 9 5 6 7 7 4 1 0 0 5 7

dyads_m9_shift0 (dyads_m9)
; dyads_m9 versus dyads_m9; m=1/1; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; wwTAAwrhwymAAAaw ; cor=; Ncor= a 11 9 0 23 23 9 9 6 9 4 8 22 23 23 11 9 c 3 5 0 0 0 1 1 8 2 7 6 0 0 0 3 5 g 2 2 0 0 0 4 8 3 5 5 5 0 0 0 4 2 t 7 7 23 0 0 9 5 6 7 7 4 1 0 0 5 7

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=24; shift=0; ncol=24; vkACTvbmsvbsmrmtysrGCGkh ; Alignment reference a 6 3 24 0 0 7 4 7 4 6 4 5 7 8 7 4 4 4 10 0 0 1 5 6 c 8 5 0 23 1 6 7 11 7 7 8 7 8 5 11 5 6 6 4 0 22 0 5 7 g 7 10 0 1 0 6 6 3 10 6 6 8 4 6 3 5 4 9 7 24 0 22 6 1 t 3 6 0 0 23 5 7 3 3 5 6 4 5 5 3 10 10 5 3 0 2 1 8 10

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/1; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; vkACTvbmsvbsmrmtysrGCGkh ; cor=; Ncor= a 6 3 24 0 0 7 4 7 4 6 4 5 7 8 7 4 4 4 10 0 0 1 5 6 c 8 5 0 23 1 6 7 11 7 7 8 7 8 5 11 5 6 6 4 0 22 0 5 7 g 7 10 0 1 0 6 6 3 10 6 6 8 4 6 3 5 4 9 7 24 0 22 6 1 t 3 6 0 0 23 5 7 3 3 5 6 4 5 5 3 10 10 5 3 0 2 1 8 10

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift3 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=24; shift=3; ncol=27; ---rvwamyrTCGATASTATCGAydrw ; Alignment reference a 0 0 0 6 5 11 11 7 2 11 1 0 0 17 1 17 0 0 17 1 0 2 14 3 5 5 5 c 0 0 0 3 6 2 1 7 8 2 3 18 0 0 0 0 5 1 1 1 17 1 2 5 2 3 4 g 0 0 0 8 6 1 3 2 4 5 1 0 19 1 1 0 13 0 1 1 0 15 1 2 7 8 4 t 0 0 0 2 2 5 4 3 5 1 14 1 0 1 17 2 1 18 0 16 2 1 2 9 5 3 6

oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---rvwamyrTCGATASTATCGAydrw ; cor=; Ncor= a 0 0 0 6 5 11 11 7 2 11 1 0 0 17 1 17 0 0 17 1 0 2 14 3 5 5 5 c 0 0 0 3 6 2 1 7 8 2 3 18 0 0 0 0 5 1 1 1 17 1 2 5 2 3 4 g 0 0 0 8 6 1 3 2 4 5 1 0 19 1 1 0 13 0 1 1 0 15 1 2 7 8 4 t 0 0 0 2 2 5 4 3 5 1 14 1 0 1 17 2 1 18 0 16 2 1 2 9 5 3 6

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=2/10; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.904547; --yvsawmyatCGATAsTATCGAtwg- ; cor=; Ncor= a 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 7 5 0 c 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 5 3 0 g 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 5 12 0 t 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13 6 3 0

dyads_m2_shift4 (dyads_m2)
; oligos_7nt_mkv2_m2 versus dyads_m2; m=3/10; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.90157; ----saahbrTCGATAsTATCGAtrdr ; cor=; Ncor= a 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 5 4 6 c 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 3 2 3 g 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 5 6 4 t 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10 3 4 3

oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=4/10; ncol2=21; w=0; offset=1; strand=D; shift=4; score=0.859793; ----swwmyaTCGATAsTATCGAth-- ; cor=; Ncor= a 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 6 0 0 c 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 6 0 0 g 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 5 0 0 t 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11 6 0 0

dyads_m7_rc_shift1 (dyads_m7_rc)
; oligos_7nt_mkv2_m2 versus dyads_m7_rc; m=5/10; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.753248; -wyRhwaswATCGATAsTATCGwsw-- ; cor=; Ncor= a 0 5 1 3 6 4 7 1 3 9 1 0 0 10 0 11 0 0 11 1 0 1 7 2 4 0 0 c 0 1 8 0 3 0 2 6 1 1 1 12 0 0 1 0 7 0 0 0 10 0 0 4 2 0 0 g 0 0 0 9 0 0 2 5 1 1 0 0 12 1 0 0 5 1 0 2 0 11 2 4 1 0 0 t 0 6 3 0 3 8 1 0 7 1 10 0 0 1 11 1 0 11 1 9 2 0 3 2 5 0 0

oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5_rc; m=6/10; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.740443; -tcGaTActATCGATAgTAtCGagt-- ; cor=; Ncor= a 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 3 0 2 8 4 4 0 0 c 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 0 15 1 2 4 3 0 0 g 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 4 1 14 4 5 4 0 0 t 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4 10 1 0 3 4 6 0 0

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=7/10; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.668967; stCGmTActATCGATagTAkCGas--- ; cor=; Ncor= a 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 0 0 0 c 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 0 0 0 g 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 0 0 0 t 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3 0 0 0

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=8/10; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.662242; kyCGmTACwATCGATwGTAkCGrm--- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 0 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 0 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 0 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0 0 0

dyads_m1_shift0 (dyads_m1)
; oligos_7nt_mkv2_m2 versus dyads_m1; m=9/10; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.662242; kyCGmTACwATCGATwGTAkCGrm--- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 0 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 0 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 0 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0 0 0

positions_6nt_m1_shift8 (positions_6nt_m1)
; oligos_7nt_mkv2_m2 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=5; strand=D; shift=8; score=0.413795; --------haTCGATAGyw-------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift3 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=24; shift=3; ncol=27; ---kyCGmTACwATCGATwGTAkCGrm ; Alignment reference a 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4
oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1)				; dyads_m1 versus oligos_6nt_mkv2_m1; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---kyCGmTACwATCGATwGTAkCGrm ; cor=; Ncor= a 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4
dyads_m1_shift3 (dyads_m1)				; dyads_m1 versus dyads_m1; m=2/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---kyCGmTACwATCGATwGTAkCGrm ; cor=; Ncor= a 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4
oligos_7nt_mkv2_m1_shift3 (oligos_7nt_mkv2_m1)				; dyads_m1 versus oligos_7nt_mkv2_m1; m=3/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.991257; ---stCGmTActATCGATagTAkCGas ; cor=; Ncor= a 0 0 0 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 c 0 0 0 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 g 0 0 0 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 t 0 0 0 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3
oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)				; dyads_m1 versus oligos_7nt_mkv2_m5_rc; m=4/10; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.905742; ----tcGaTActATCGATAgTAtCGag ; cor=; Ncor= a 0 0 0 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 3 0 2 8 4 c 0 0 0 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 0 15 1 2 4 g 0 0 0 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 4 1 14 4 5 t 0 0 0 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4 10 1 0 3 4
dyads_m7_shift2 (dyads_m7)				; dyads_m1 versus dyads_m7; m=5/10; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.864696; --wswCGATAsTATCGATwstwdYrw- ; cor=; Ncor= a 0 0 5 2 3 0 2 9 1 11 0 1 11 1 0 0 10 1 7 0 1 8 3 0 3 6 0 c 0 0 1 4 2 11 0 2 0 1 5 0 0 1 12 0 0 1 1 5 2 0 0 9 0 0 0 g 0 0 2 4 0 0 10 0 0 0 7 0 1 0 0 12 1 1 1 6 2 0 3 0 8 1 0 t 0 0 4 2 7 1 0 1 11 0 0 11 0 10 0 0 1 9 3 1 7 4 6 3 1 5 0
oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2_rc)				; dyads_m1 versus oligos_6nt_mkv2_m2_rc; m=6/10; ncol2=21; w=-1; offset=-1; strand=R; shift=2; score=0.681035; --daTCGATAsTATCGAtrkwws---- ; cor=; Ncor= a 0 0 6 11 2 0 1 21 0 22 1 2 21 1 0 1 16 3 7 5 6 6 5 0 0 0 0 c 0 0 5 3 2 21 0 1 0 0 14 0 2 0 22 0 1 5 4 4 3 3 7 0 0 0 0 g 0 0 6 5 3 1 22 0 2 1 7 0 0 0 0 22 4 2 8 8 4 4 7 0 0 0 0 t 0 0 6 4 16 1 0 1 21 0 1 21 0 22 1 0 2 13 4 6 10 10 4 0 0 0 0
oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)				; dyads_m1 versus oligos_7nt_mkv2_m4; m=7/10; ncol2=24; w=0; offset=2; strand=D; shift=5; score=0.670121; -----yvsawmyatCGATAsTATCGAt ; cor=; Ncor= a 0 0 0 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 c 0 0 0 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 g 0 0 0 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 t 0 0 0 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; dyads_m1 versus oligos_7nt_mkv2_m2_rc; m=8/10; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.662242; wyhrTCGATASTATCGAyrktwby--- ; cor=; Ncor= a 6 3 5 9 2 1 2 16 0 18 1 2 17 1 0 1 14 1 5 3 4 5 2 2 0 0 0 c 4 8 7 2 1 15 0 1 1 0 13 0 1 1 19 0 1 5 4 2 3 1 6 8 0 0 0 g 4 3 2 5 2 1 17 1 1 1 5 0 0 0 0 18 3 2 8 7 1 2 6 3 0 0 0 t 5 5 5 3 14 2 0 1 17 0 0 17 1 17 0 0 1 11 2 7 11 11 5 6 0 0 0
dyads_m2_shift7 (dyads_m2)				; dyads_m1 versus dyads_m2; m=9/10; ncol2=24; w=0; offset=4; strand=D; shift=7; score=0.584379; -------saahbrTCGATAsTATCGAt ; cor=; Ncor= a 0 0 0 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 c 0 0 0 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 g 0 0 0 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 t 0 0 0 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10
positions_6nt_m1_shift11 (positions_6nt_m1)				; dyads_m1 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=8; strand=D; shift=11; score=0.415907; -----------haTCGATAGyw----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=24; shift=3; ncol=27; ---kyCGmTACwATCGATwGTAkCGrm ; Alignment reference a 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4
oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---kyCGmTACwATCGATwGTAkCGrm ; cor=; Ncor= a 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4
dyads_m1_shift3 (dyads_m1)				; oligos_6nt_mkv2_m1 versus dyads_m1; m=2/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---kyCGmTACwATCGATwGTAkCGrm ; cor=; Ncor= a 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4
oligos_7nt_mkv2_m1_shift3 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.991257; ---stCGmTActATCGATagTAkCGas ; cor=; Ncor= a 0 0 0 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 c 0 0 0 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 g 0 0 0 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 t 0 0 0 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3
oligos_7nt_mkv2_m5_rc_shift4 (oligos_7nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5_rc; m=4/10; ncol2=24; w=0; offset=1; strand=R; shift=4; score=0.905742; ----tcGaTActATCGATAgTAtCGag ; cor=; Ncor= a 0 0 0 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 3 0 2 8 4 c 0 0 0 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 0 15 1 2 4 g 0 0 0 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 4 1 14 4 5 t 0 0 0 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4 10 1 0 3 4
dyads_m7_shift2 (dyads_m7)				; oligos_6nt_mkv2_m1 versus dyads_m7; m=5/10; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.864696; --wswCGATAsTATCGATwstwdYrw- ; cor=; Ncor= a 0 0 5 2 3 0 2 9 1 11 0 1 11 1 0 0 10 1 7 0 1 8 3 0 3 6 0 c 0 0 1 4 2 11 0 2 0 1 5 0 0 1 12 0 0 1 1 5 2 0 0 9 0 0 0 g 0 0 2 4 0 0 10 0 0 0 7 0 1 0 0 12 1 1 1 6 2 0 3 0 8 1 0 t 0 0 4 2 7 1 0 1 11 0 0 11 0 10 0 0 1 9 3 1 7 4 6 3 1 5 0
oligos_6nt_mkv2_m2_rc_shift2 (oligos_6nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=6/10; ncol2=21; w=-1; offset=-1; strand=R; shift=2; score=0.681035; --daTCGATAsTATCGAtrkwws---- ; cor=; Ncor= a 0 0 6 11 2 0 1 21 0 22 1 2 21 1 0 1 16 3 7 5 6 6 5 0 0 0 0 c 0 0 5 3 2 21 0 1 0 0 14 0 2 0 22 0 1 5 4 4 3 3 7 0 0 0 0 g 0 0 6 5 3 1 22 0 2 1 7 0 0 0 0 22 4 2 8 8 4 4 7 0 0 0 0 t 0 0 6 4 16 1 0 1 21 0 1 21 0 22 1 0 2 13 4 6 10 10 4 0 0 0 0
oligos_7nt_mkv2_m4_shift5 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=7/10; ncol2=24; w=0; offset=2; strand=D; shift=5; score=0.670121; -----yvsawmyatCGATAsTATCGAt ; cor=; Ncor= a 0 0 0 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 c 0 0 0 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 g 0 0 0 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 t 0 0 0 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13
oligos_7nt_mkv2_m2_rc_shift0 (oligos_7nt_mkv2_m2_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=8/10; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.662242; wyhrTCGATASTATCGAyrktwby--- ; cor=; Ncor= a 6 3 5 9 2 1 2 16 0 18 1 2 17 1 0 1 14 1 5 3 4 5 2 2 0 0 0 c 4 8 7 2 1 15 0 1 1 0 13 0 1 1 19 0 1 5 4 2 3 1 6 8 0 0 0 g 4 3 2 5 2 1 17 1 1 1 5 0 0 0 0 18 3 2 8 7 1 2 6 3 0 0 0 t 5 5 5 3 14 2 0 1 17 0 0 17 1 17 0 0 1 11 2 7 11 11 5 6 0 0 0
dyads_m2_shift7 (dyads_m2)				; oligos_6nt_mkv2_m1 versus dyads_m2; m=9/10; ncol2=24; w=0; offset=4; strand=D; shift=7; score=0.584379; -------saahbrTCGATAsTATCGAt ; cor=; Ncor= a 0 0 0 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 c 0 0 0 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 g 0 0 0 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 t 0 0 0 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10
positions_6nt_m1_shift11 (positions_6nt_m1)				; oligos_6nt_mkv2_m1 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=8; strand=D; shift=11; score=0.415907; -----------haTCGATAGyw----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=2; ncol=12; --rwAAAATAww ; Alignment reference a 0 0 12 13 35 35 35 35 0 35 10 10 c 0 0 5 6 0 0 0 0 0 0 8 8 g 0 0 10 6 0 0 0 0 0 0 4 7 t 0 0 8 10 0 0 0 0 35 0 13 10
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score= 1; --rwAAAATAww ; cor=; Ncor= a 0 0 12 13 35 35 35 35 0 35 10 10 c 0 0 5 6 0 0 0 0 0 0 8 8 g 0 0 10 6 0 0 0 0 0 0 4 7 t 0 0 8 10 0 0 0 0 35 0 13 10
dyads_m3_shift1 (dyads_m3)				; oligos_6nt_mkv2_m3 versus dyads_m3; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score= 0.9071; -wrwAAAATAww ; cor=; Ncor= a 0 14 13 13 38 38 35 38 0 38 11 11 c 0 8 7 6 0 0 0 0 0 0 9 8 g 0 1 10 6 0 0 0 0 0 0 5 8 t 0 15 8 13 0 0 3 0 38 0 13 11
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=3/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.631862; twaATAAATAww ; cor=; Ncor= a 8 14 24 40 3 37 35 40 2 38 13 11 c 7 10 3 1 2 1 0 0 1 1 9 8 g 6 4 4 0 4 1 2 1 0 1 5 10 t 20 13 10 0 32 2 4 0 38 1 14 12

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m7_shift3 (dyads_m7)				; dyads_m7; m=0 (reference); ncol1=24; shift=3; ncol=27; ---wswCGATAsTATCGATwstwdYrw ; Alignment reference a 0 0 0 5 2 3 0 2 9 1 11 0 1 11 1 0 0 10 1 7 0 1 8 3 0 3 6 c 0 0 0 1 4 2 11 0 2 0 1 5 0 0 1 12 0 0 1 1 5 2 0 0 9 0 0 g 0 0 0 2 4 0 0 10 0 0 0 7 0 1 0 0 12 1 1 1 6 2 0 3 0 8 1 t 0 0 0 4 2 7 1 0 1 11 0 0 11 0 10 0 0 1 9 3 1 7 4 6 3 1 5
dyads_m7_shift3 (dyads_m7)				; dyads_m7 versus dyads_m7; m=1/9; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---wswCGATAsTATCGATwstwdYrw ; cor=; Ncor= a 0 0 0 5 2 3 0 2 9 1 11 0 1 11 1 0 0 10 1 7 0 1 8 3 0 3 6 c 0 0 0 1 4 2 11 0 2 0 1 5 0 0 1 12 0 0 1 1 5 2 0 0 9 0 0 g 0 0 0 2 4 0 0 10 0 0 0 7 0 1 0 0 12 1 1 1 6 2 0 3 0 8 1 t 0 0 0 4 2 7 1 0 1 11 0 0 11 0 10 0 0 1 9 3 1 7 4 6 3 1 5
oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)				; dyads_m7 versus oligos_7nt_mkv2_m5; m=2/9; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.950765; ---actCGaTAcTATCGATagTAtCga ; cor=; Ncor= a 0 0 0 6 4 3 0 1 10 4 14 2 2 15 1 0 1 15 0 11 1 2 12 4 0 2 10 c 0 0 0 4 5 4 14 1 4 0 1 11 3 1 1 16 0 0 1 0 4 1 1 0 12 4 1 g 0 0 0 3 4 2 1 15 0 1 1 4 0 1 0 0 16 1 1 2 10 2 0 4 2 11 3 t 0 0 0 4 4 8 2 0 3 12 1 0 12 0 15 1 0 1 15 4 2 12 4 9 3 0 3
oligos_7nt_mkv2_m1_shift4 (oligos_7nt_mkv2_m1)				; dyads_m7 versus oligos_7nt_mkv2_m1; m=3/9; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.866355; ----stCGmTActATCGATagTAkCGa ; cor=; Ncor= a 0 0 0 0 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 c 0 0 0 0 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 g 0 0 0 0 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 t 0 0 0 0 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3
dyads_m1_shift4 (dyads_m1)				; dyads_m7 versus dyads_m1; m=4/9; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.864696; ----kyCGmTACwATCGATwGTAkCGr ; cor=; Ncor= a 0 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 c 0 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 g 0 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 t 0 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4
oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)				; dyads_m7 versus oligos_6nt_mkv2_m1; m=5/9; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.864696; ----kyCGmTACwATCGATwGTAkCGr ; cor=; Ncor= a 0 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 c 0 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 g 0 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 t 0 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4
oligos_7nt_mkv2_m4_rc_shift2 (oligos_7nt_mkv2_m4_rc)				; dyads_m7 versus oligos_7nt_mkv2_m4_rc; m=6/9; ncol2=24; w=-1; offset=-1; strand=R; shift=2; score=0.796152; --cwaTCGATAsTATCGatrkwtsbr- ; cor=; Ncor= a 0 0 3 6 13 2 1 2 20 0 21 1 1 21 1 0 0 15 2 6 4 6 3 4 3 8 0 c 0 0 12 5 3 2 20 0 0 2 0 15 0 1 1 22 0 1 5 4 4 3 3 8 8 4 0 g 0 0 3 5 5 2 1 21 2 1 1 7 0 0 0 0 23 5 4 9 8 4 4 7 6 7 0 t 0 0 5 7 2 17 1 0 1 20 1 0 22 1 21 1 0 2 12 4 7 10 13 4 6 4 0
oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)				; dyads_m7 versus oligos_6nt_mkv2_m2_rc; m=7/9; ncol2=21; w=0; offset=0; strand=R; shift=3; score=0.794986; ---daTCGATAsTATCGAtrkwws--- ; cor=; Ncor= a 0 0 0 6 11 2 0 1 21 0 22 1 2 21 1 0 1 16 3 7 5 6 6 5 0 0 0 c 0 0 0 5 3 2 21 0 1 0 0 14 0 2 0 22 0 1 5 4 4 3 3 7 0 0 0 g 0 0 0 6 5 3 1 22 0 2 1 7 0 0 0 0 22 4 2 8 8 4 4 7 0 0 0 t 0 0 0 6 4 16 1 0 1 21 0 1 21 0 22 1 0 2 13 4 6 10 10 4 0 0 0
oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)				; dyads_m7 versus oligos_7nt_mkv2_m2_rc; m=8/9; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.753248; -wyhrTCGATASTATCGAyrktwby-- ; cor=; Ncor= a 0 6 3 5 9 2 1 2 16 0 18 1 2 17 1 0 1 14 1 5 3 4 5 2 2 0 0 c 0 4 8 7 2 1 15 0 1 1 0 13 0 1 1 19 0 1 5 4 2 3 1 6 8 0 0 g 0 4 3 2 5 2 1 17 1 1 1 5 0 0 0 0 18 3 2 8 7 1 2 6 3 0 0 t 0 5 5 5 3 14 2 0 1 17 0 0 17 1 17 0 0 1 11 2 7 11 11 5 6 0 0
dyads_m2_rc_shift0 (dyads_m2_rc)				; dyads_m7 versus dyads_m2_rc; m=9/9; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.680859; ayhyaTCGATAsTATCGAyvdtts--- ; cor=; Ncor= a 8 3 4 3 10 0 1 1 15 0 16 0 1 13 1 0 1 12 1 4 4 3 3 2 0 0 0 c 2 4 6 5 0 1 15 0 0 0 0 10 0 2 1 16 0 1 4 4 1 3 3 5 0 0 0 g 3 3 2 3 3 2 0 15 0 1 0 6 0 0 0 0 15 2 2 6 6 3 2 6 0 0 0 t 3 6 4 5 3 13 0 0 1 15 0 0 15 1 14 0 0 1 9 2 5 7 8 3 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift1 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -wrwAAAATAww ; Alignment reference a 0 14 13 13 38 38 35 38 0 38 11 11 c 0 8 7 6 0 0 0 0 0 0 9 8 g 0 1 10 6 0 0 0 0 0 0 5 8 t 0 15 8 13 0 0 3 0 38 0 13 11
dyads_m3_shift1 (dyads_m3)				; dyads_m3 versus dyads_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -wrwAAAATAww ; cor=; Ncor= a 0 14 13 13 38 38 35 38 0 38 11 11 c 0 8 7 6 0 0 0 0 0 0 9 8 g 0 1 10 6 0 0 0 0 0 0 5 8 t 0 15 8 13 0 0 3 0 38 0 13 11
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)				; dyads_m3 versus oligos_6nt_mkv2_m3; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=2; score= 0.9071; --rwAAAATAww ; cor=; Ncor= a 0 0 12 13 35 35 35 35 0 35 10 10 c 0 0 5 6 0 0 0 0 0 0 8 8 g 0 0 10 6 0 0 0 0 0 0 4 7 t 0 0 8 10 0 0 0 0 35 0 13 10
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; dyads_m3 versus oligos_7nt_mkv2_m3; m=3/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.688871; twaATAAATAww ; cor=; Ncor= a 8 14 24 40 3 37 35 40 2 38 13 11 c 7 10 3 1 2 1 0 0 1 1 9 8 g 6 4 4 0 4 1 2 1 0 1 5 10 t 20 13 10 0 32 2 4 0 38 1 14 12

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=21; shift=4; ncol=25; ----swwmyaTCGATAsTATCGAth ; Alignment reference a 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 6 c 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 6 g 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 5 t 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11 6
oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/10; ncol2=21; w=0; offset=0; strand=D; shift=4; score= 1; ----swwmyaTCGATAsTATCGAth ; cor=; Ncor= a 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 6 c 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 6 g 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 5 t 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11 6
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=2/10; ncol2=24; w=-2; offset=-2; strand=D; shift=2; score=0.866938; --yvsawmyatCGATAsTATCGAtw ; cor=; Ncor= a 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 7 c 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 5 g 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 5 t 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13 6
dyads_m2_shift4 (dyads_m2)				; oligos_6nt_mkv2_m2 versus dyads_m2; m=3/10; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.862825; ----saahbrTCGATAsTATCGAtr ; cor=; Ncor= a 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 5 c 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 3 g 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 5 t 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10 3
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=4/10; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.859793; ---rvwamyrTCGATASTATCGAyd ; cor=; Ncor= a 0 0 0 6 5 11 11 7 2 11 1 0 0 17 1 17 0 0 17 1 0 2 14 3 5 c 0 0 0 3 6 2 1 7 8 2 3 18 0 0 0 0 5 1 1 1 17 1 2 5 2 g 0 0 0 8 6 1 3 2 4 5 1 0 19 1 1 0 13 0 1 1 0 15 1 2 7 t 0 0 0 2 2 5 4 3 5 1 14 1 0 1 17 2 1 18 0 16 2 1 2 9 5
dyads_m7_rc_shift1 (dyads_m7_rc)				; oligos_6nt_mkv2_m2 versus dyads_m7_rc; m=5/10; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.794986; -wyRhwaswATCGATAsTATCGwsw ; cor=; Ncor= a 0 5 1 3 6 4 7 1 3 9 1 0 0 10 0 11 0 0 11 1 0 1 7 2 4 c 0 1 8 0 3 0 2 6 1 1 1 12 0 0 1 0 7 0 0 0 10 0 0 4 2 g 0 0 0 9 0 0 2 5 1 1 0 0 12 1 0 0 5 1 0 2 0 11 2 4 1 t 0 6 3 0 3 8 1 0 7 1 10 0 0 1 11 1 0 11 1 9 2 0 3 2 5
oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m5_rc; m=6/10; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.772413; -tcGaTActATCGATAgTAtCGagt ; cor=; Ncor= a 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 3 0 2 8 4 4 c 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 0 15 1 2 4 3 g 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 4 1 14 4 5 4 t 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4 10 1 0 3 4 6
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=7/10; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.688257; stCGmTActATCGATagTAkCGas- ; cor=; Ncor= a 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 0 c 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 0 g 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 0 t 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3 0
dyads_m1_shift0 (dyads_m1)				; oligos_6nt_mkv2_m2 versus dyads_m1; m=8/10; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.681035; kyCGmTACwATCGATwGTAkCGrm- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=9/10; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.681035; kyCGmTACwATCGATwGTAkCGrm- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0
positions_6nt_m1_shift8 (positions_6nt_m1)				; oligos_6nt_mkv2_m2 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=4; strand=D; shift=8; score=0.471129; --------haTCGATAGyw------ ; cor=; Ncor= a 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift4 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=24; shift=4; ncol=28; ----saahbrTCGATAsTATCGAtrdrt ; Alignment reference a 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 5 4 6 3 c 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 3 2 3 3 g 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 5 6 4 2 t 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10 3 4 3 8
dyads_m2_shift4 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----saahbrTCGATAsTATCGAtrdrt ; cor=; Ncor= a 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 5 4 6 3 c 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 3 2 3 3 g 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 5 6 4 2 t 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10 3 4 3 8
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; dyads_m2 versus oligos_7nt_mkv2_m2; m=2/10; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.90157; ---rvwamyrTCGATASTATCGAydrw- ; cor=; Ncor= a 0 0 0 6 5 11 11 7 2 11 1 0 0 17 1 17 0 0 17 1 0 2 14 3 5 5 5 0 c 0 0 0 3 6 2 1 7 8 2 3 18 0 0 0 0 5 1 1 1 17 1 2 5 2 3 4 0 g 0 0 0 8 6 1 3 2 4 5 1 0 19 1 1 0 13 0 1 1 0 15 1 2 7 8 4 0 t 0 0 0 2 2 5 4 3 5 1 14 1 0 1 17 2 1 18 0 16 2 1 2 9 5 3 6 0
oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)				; dyads_m2 versus oligos_6nt_mkv2_m2; m=3/10; ncol2=21; w=0; offset=0; strand=D; shift=4; score=0.862825; ----swwmyaTCGATAsTATCGAth--- ; cor=; Ncor= a 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 6 0 0 0 c 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 6 0 0 0 g 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 5 0 0 0 t 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11 6 0 0 0
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; dyads_m2 versus oligos_7nt_mkv2_m4; m=4/10; ncol2=24; w=-2; offset=-2; strand=D; shift=2; score=0.831938; --yvsawmyatCGATAsTATCGAtwg-- ; cor=; Ncor= a 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 7 5 0 0 c 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 5 3 0 0 g 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 5 12 0 0 t 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13 6 3 0 0
dyads_m7_rc_shift1 (dyads_m7_rc)				; dyads_m2 versus dyads_m7_rc; m=5/10; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.680859; -wyRhwaswATCGATAsTATCGwsw--- ; cor=; Ncor= a 0 5 1 3 6 4 7 1 3 9 1 0 0 10 0 11 0 0 11 1 0 1 7 2 4 0 0 0 c 0 1 8 0 3 0 2 6 1 1 1 12 0 0 1 0 7 0 0 0 10 0 0 4 2 0 0 0 g 0 0 0 9 0 0 2 5 1 1 0 0 12 1 0 0 5 1 0 2 0 11 2 4 1 0 0 0 t 0 6 3 0 3 8 1 0 7 1 10 0 0 1 11 1 0 11 1 9 2 0 3 2 5 0 0 0
oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)				; dyads_m2 versus oligos_7nt_mkv2_m5_rc; m=6/10; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.65843; -tcGaTActATCGATAgTAtCGagt--- ; cor=; Ncor= a 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 3 0 2 8 4 4 0 0 0 c 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 0 15 1 2 4 3 0 0 0 g 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 4 1 14 4 5 4 0 0 0 t 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4 10 1 0 3 4 6 0 0 0
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; dyads_m2 versus oligos_7nt_mkv2_m1; m=7/10; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.590481; stCGmTActATCGATagTAkCGas---- ; cor=; Ncor= a 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 0 0 0 0 c 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 0 0 0 0 g 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 0 0 0 0 t 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3 0 0 0 0
dyads_m1_shift0 (dyads_m1)				; dyads_m2 versus dyads_m1; m=8/10; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.584379; kyCGmTACwATCGATwGTAkCGrm---- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 0 0 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 0 0 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 0 0 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0 0 0 0
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; dyads_m2 versus oligos_6nt_mkv2_m1; m=9/10; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.584379; kyCGmTACwATCGATwGTAkCGrm---- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 0 0 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 0 0 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 0 0 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0 0 0 0
positions_6nt_m1_shift8 (positions_6nt_m1)				; dyads_m2 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=4; strand=D; shift=8; score=0.403924; --------haTCGATAGyw--------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift8 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=11; shift=8; ncol=19; --------haTCGATAGyw ; Alignment reference a 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 c 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 g 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 t 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28
positions_6nt_m1_shift8 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/9; ncol2=11; w=0; offset=0; strand=D; shift=8; score= 1; --------haTCGATAGyw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 c 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 g 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 t 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28
oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)				; positions_6nt_m1 versus oligos_6nt_mkv2_m2; m=2/9; ncol2=21; w=-4; offset=-4; strand=D; shift=4; score=0.471129; ----swwmyaTCGATAsTA ; cor=; Ncor= a 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 c 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 g 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 t 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0
oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)				; positions_6nt_m1 versus oligos_7nt_mkv2_m5_rc; m=3/9; ncol2=24; w=-7; offset=-7; strand=R; shift=1; score=0.41645; -tcGaTActATCGATAgTA ; cor=; Ncor= a 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 c 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 g 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 t 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; positions_6nt_m1 versus oligos_7nt_mkv2_m1; m=4/9; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.41602; stCGmTActATCGATagTA ; cor=; Ncor= a 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 c 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 g 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 t 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; positions_6nt_m1 versus oligos_6nt_mkv2_m1; m=5/9; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.415907; kyCGmTACwATCGATwGTA ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5
dyads_m1_shift0 (dyads_m1)				; positions_6nt_m1 versus dyads_m1; m=6/9; ncol2=24; w=-8; offset=-8; strand=D; shift=0; score=0.415907; kyCGmTACwATCGATwGTA ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; positions_6nt_m1 versus oligos_7nt_mkv2_m4; m=7/9; ncol2=24; w=-6; offset=-6; strand=D; shift=2; score=0.415068; --yvsawmyatCGATAsTA ; cor=; Ncor= a 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 c 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 g 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 t 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; positions_6nt_m1 versus oligos_7nt_mkv2_m2; m=8/9; ncol2=24; w=-5; offset=-5; strand=D; shift=3; score=0.413795; ---rvwamyrTCGATASTA ; cor=; Ncor= a 0 0 0 6 5 11 11 7 2 11 1 0 0 17 1 17 0 0 17 c 0 0 0 3 6 2 1 7 8 2 3 18 0 0 0 0 5 1 1 g 0 0 0 8 6 1 3 2 4 5 1 0 19 1 1 0 13 0 1 t 0 0 0 2 2 5 4 3 5 1 14 1 0 1 17 2 1 18 0
dyads_m2_shift4 (dyads_m2)				; positions_6nt_m1 versus dyads_m2; m=9/9; ncol2=24; w=-4; offset=-4; strand=D; shift=4; score=0.403924; ----saahbrTCGATAsTA ; cor=; Ncor= a 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 c 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 g 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 t 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=24; shift=3; ncol=27; ---actCGaTAcTATCGATagTAtCga ; Alignment reference a 0 0 0 6 4 3 0 1 10 4 14 2 2 15 1 0 1 15 0 11 1 2 12 4 0 2 10 c 0 0 0 4 5 4 14 1 4 0 1 11 3 1 1 16 0 0 1 0 4 1 1 0 12 4 1 g 0 0 0 3 4 2 1 15 0 1 1 4 0 1 0 0 16 1 1 2 10 2 0 4 2 11 3 t 0 0 0 4 4 8 2 0 3 12 1 0 12 0 15 1 0 1 15 4 2 12 4 9 3 0 3
oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---actCGaTAcTATCGATagTAtCga ; cor=; Ncor= a 0 0 0 6 4 3 0 1 10 4 14 2 2 15 1 0 1 15 0 11 1 2 12 4 0 2 10 c 0 0 0 4 5 4 14 1 4 0 1 11 3 1 1 16 0 0 1 0 4 1 1 0 12 4 1 g 0 0 0 3 4 2 1 15 0 1 1 4 0 1 0 0 16 1 1 2 10 2 0 4 2 11 3 t 0 0 0 4 4 8 2 0 3 12 1 0 12 0 15 1 0 1 15 4 2 12 4 9 3 0 3
dyads_m7_shift3 (dyads_m7)				; oligos_7nt_mkv2_m5 versus dyads_m7; m=2/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score=0.950765; ---wswCGATAsTATCGATwstwdYrw ; cor=; Ncor= a 0 0 0 5 2 3 0 2 9 1 11 0 1 11 1 0 0 10 1 7 0 1 8 3 0 3 6 c 0 0 0 1 4 2 11 0 2 0 1 5 0 0 1 12 0 0 1 1 5 2 0 0 9 0 0 g 0 0 0 2 4 0 0 10 0 0 0 7 0 1 0 0 12 1 1 1 6 2 0 3 0 8 1 t 0 0 0 4 2 7 1 0 1 11 0 0 11 0 10 0 0 1 9 3 1 7 4 6 3 1 5
oligos_7nt_mkv2_m1_shift4 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=3/10; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.911191; ----stCGmTActATCGATagTAkCGa ; cor=; Ncor= a 0 0 0 0 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 c 0 0 0 0 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 g 0 0 0 0 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 t 0 0 0 0 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3
oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=4/10; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.905742; ----kyCGmTACwATCGATwGTAkCGr ; cor=; Ncor= a 0 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 c 0 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 g 0 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 t 0 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4
dyads_m1_shift4 (dyads_m1)				; oligos_7nt_mkv2_m5 versus dyads_m1; m=5/10; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.905742; ----kyCGmTACwATCGATwGTAkCGr ; cor=; Ncor= a 0 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 c 0 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 g 0 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 t 0 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4
oligos_6nt_mkv2_m2_rc_shift3 (oligos_6nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m2_rc; m=6/10; ncol2=21; w=0; offset=0; strand=R; shift=3; score=0.772413; ---daTCGATAsTATCGAtrkwws--- ; cor=; Ncor= a 0 0 0 6 11 2 0 1 21 0 22 1 2 21 1 0 1 16 3 7 5 6 6 5 0 0 0 c 0 0 0 5 3 2 21 0 1 0 0 14 0 2 0 22 0 1 5 4 4 3 3 7 0 0 0 g 0 0 0 6 5 3 1 22 0 2 1 7 0 0 0 0 22 4 2 8 8 4 4 7 0 0 0 t 0 0 0 6 4 16 1 0 1 21 0 1 21 0 22 1 0 2 13 4 6 10 10 4 0 0 0
oligos_7nt_mkv2_m4_rc_shift2 (oligos_7nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m4_rc; m=7/10; ncol2=24; w=-1; offset=-1; strand=R; shift=2; score=0.765826; --cwaTCGATAsTATCGatrkwtsbr- ; cor=; Ncor= a 0 0 3 6 13 2 1 2 20 0 21 1 1 21 1 0 0 15 2 6 4 6 3 4 3 8 0 c 0 0 12 5 3 2 20 0 0 2 0 15 0 1 1 22 0 1 5 4 4 3 3 8 8 4 0 g 0 0 3 5 5 2 1 21 2 1 1 7 0 0 0 0 23 5 4 9 8 4 4 7 6 7 0 t 0 0 5 7 2 17 1 0 1 20 1 0 22 1 21 1 0 2 12 4 7 10 13 4 6 4 0
oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m2_rc; m=8/10; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.740443; -wyhrTCGATASTATCGAyrktwby-- ; cor=; Ncor= a 0 6 3 5 9 2 1 2 16 0 18 1 2 17 1 0 1 14 1 5 3 4 5 2 2 0 0 c 0 4 8 7 2 1 15 0 1 1 0 13 0 1 1 19 0 1 5 4 2 3 1 6 8 0 0 g 0 4 3 2 5 2 1 17 1 1 1 5 0 0 0 0 18 3 2 8 7 1 2 6 3 0 0 t 0 5 5 5 3 14 2 0 1 17 0 0 17 1 17 0 0 1 11 2 7 11 11 5 6 0 0
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv2_m5 versus dyads_m2_rc; m=9/10; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.65843; ayhyaTCGATAsTATCGAyvdtts--- ; cor=; Ncor= a 8 3 4 3 10 0 1 1 15 0 16 0 1 13 1 0 1 12 1 4 4 3 3 2 0 0 0 c 2 4 6 5 0 1 15 0 0 0 0 10 0 2 1 16 0 1 4 4 1 3 3 5 0 0 0 g 3 3 2 3 3 2 0 15 0 1 0 6 0 0 0 0 15 2 2 6 6 3 2 6 0 0 0 t 3 6 4 5 3 13 0 0 1 15 0 0 15 1 14 0 0 1 9 2 5 7 8 3 0 0 0
positions_6nt_m1_rc_shift9 (positions_6nt_m1_rc)				; oligos_7nt_mkv2_m5 versus positions_6nt_m1_rc; m=10/10; ncol2=11; w=0; offset=6; strand=R; shift=9; score=0.41645; ---------wrCTATCGAtd------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 28 38 4 6 79 1 1 1 74 16 25 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 14 12 69 8 3 0 86 1 4 16 14 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 15 27 12 0 2 2 1 84 5 11 24 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 31 11 3 74 4 85 0 2 5 45 25 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=24; shift=2; ncol=26; --yvsawmyatCGATAsTATCGAtwg ; Alignment reference a 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 7 5 c 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 5 3 g 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 5 12 t 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13 6 3
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=2; score= 1; --yvsawmyatCGATAsTATCGAtwg ; cor=; Ncor= a 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 7 5 c 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 5 3 g 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 5 12 t 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13 6 3
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m2; m=2/10; ncol2=24; w=0; offset=1; strand=D; shift=3; score=0.904547; ---rvwamyrTCGATASTATCGAydr ; cor=; Ncor= a 0 0 0 6 5 11 11 7 2 11 1 0 0 17 1 17 0 0 17 1 0 2 14 3 5 5 c 0 0 0 3 6 2 1 7 8 2 3 18 0 0 0 0 5 1 1 1 17 1 2 5 2 3 g 0 0 0 8 6 1 3 2 4 5 1 0 19 1 1 0 13 0 1 1 0 15 1 2 7 8 t 0 0 0 2 2 5 4 3 5 1 14 1 0 1 17 2 1 18 0 16 2 1 2 9 5 3
oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m2; m=3/10; ncol2=21; w=0; offset=2; strand=D; shift=4; score=0.866938; ----swwmyaTCGATAsTATCGAth- ; cor=; Ncor= a 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 6 0 c 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 6 0 g 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 5 0 t 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11 6 0
dyads_m2_shift4 (dyads_m2)				; oligos_7nt_mkv2_m4 versus dyads_m2; m=4/10; ncol2=24; w=0; offset=2; strand=D; shift=4; score=0.831938; ----saahbrTCGATAsTATCGAtrd ; cor=; Ncor= a 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 5 4 c 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 3 2 g 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 5 6 t 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10 3 4
dyads_m7_rc_shift1 (dyads_m7_rc)				; oligos_7nt_mkv2_m4 versus dyads_m7_rc; m=5/10; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.796152; -wyRhwaswATCGATAsTATCGwsw- ; cor=; Ncor= a 0 5 1 3 6 4 7 1 3 9 1 0 0 10 0 11 0 0 11 1 0 1 7 2 4 0 c 0 1 8 0 3 0 2 6 1 1 1 12 0 0 1 0 7 0 0 0 10 0 0 4 2 0 g 0 0 0 9 0 0 2 5 1 1 0 0 12 1 0 0 5 1 0 2 0 11 2 4 1 0 t 0 6 3 0 3 8 1 0 7 1 10 0 0 1 11 1 0 11 1 9 2 0 3 2 5 0
oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m5_rc; m=6/10; ncol2=24; w=-1; offset=-1; strand=R; shift=1; score=0.765826; -tcGaTActATCGATAgTAtCGagt- ; cor=; Ncor= a 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 3 0 2 8 4 4 0 c 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 0 15 1 2 4 3 0 g 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 4 1 14 4 5 4 0 t 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4 10 1 0 3 4 6 0
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=7/10; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.680504; stCGmTActATCGATagTAkCGas-- ; cor=; Ncor= a 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 0 0 c 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 0 0 g 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 0 0 t 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3 0 0
dyads_m1_shift0 (dyads_m1)				; oligos_7nt_mkv2_m4 versus dyads_m1; m=8/10; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.670121; kyCGmTACwATCGATwGTAkCGrm-- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0 0
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=9/10; ncol2=24; w=-2; offset=-2; strand=D; shift=0; score=0.670121; kyCGmTACwATCGATwGTAkCGrm-- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0 0
positions_6nt_m1_shift8 (positions_6nt_m1)				; oligos_7nt_mkv2_m4 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=6; strand=D; shift=8; score=0.415068; --------haTCGATAGyw------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; twaATAAATAww ; Alignment reference a 8 14 24 40 3 37 35 40 2 38 13 11 c 7 10 3 1 2 1 0 0 1 1 9 8 g 6 4 4 0 4 1 2 1 0 1 5 10 t 20 13 10 0 32 2 4 0 38 1 14 12
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; twaATAAATAww ; cor=; Ncor= a 8 14 24 40 3 37 35 40 2 38 13 11 c 7 10 3 1 2 1 0 0 1 1 9 8 g 6 4 4 0 4 1 2 1 0 1 5 10 t 20 13 10 0 32 2 4 0 38 1 14 12
dyads_m3_shift1 (dyads_m3)				; oligos_7nt_mkv2_m3 versus dyads_m3; m=2/3; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.688871; -wrwAAAATAww ; cor=; Ncor= a 0 14 13 13 38 38 35 38 0 38 11 11 c 0 8 7 6 0 0 0 0 0 0 9 8 g 0 1 10 6 0 0 0 0 0 0 5 8 t 0 15 8 13 0 0 3 0 38 0 13 11
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.631862; --rwAAAATAww ; cor=; Ncor= a 0 0 12 13 35 35 35 35 0 35 10 10 c 0 0 5 6 0 0 0 0 0 0 8 8 g 0 0 10 6 0 0 0 0 0 0 4 7 t 0 0 8 10 0 0 0 0 35 0 13 10

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift4 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=24; shift=4; ncol=28; ----stCGmTActATCGATagTAkCGas ; Alignment reference a 0 0 0 0 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 c 0 0 0 0 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 g 0 0 0 0 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 t 0 0 0 0 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3
oligos_7nt_mkv2_m1_shift4 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=4; score= 1; ----stCGmTActATCGATagTAkCGas ; cor=; Ncor= a 0 0 0 0 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 c 0 0 0 0 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 g 0 0 0 0 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 t 0 0 0 0 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3
oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/10; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.991257; ----kyCGmTACwATCGATwGTAkCGrm ; cor=; Ncor= a 0 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4
dyads_m1_shift4 (dyads_m1)				; oligos_7nt_mkv2_m1 versus dyads_m1; m=3/10; ncol2=24; w=0; offset=0; strand=D; shift=4; score=0.991257; ----kyCGmTACwATCGATwGTAkCGrm ; cor=; Ncor= a 0 0 0 0 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 c 0 0 0 0 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 g 0 0 0 0 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 t 0 0 0 0 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4
oligos_7nt_mkv2_m5_shift3 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=4/10; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.911191; ---actCGaTAcTATCGATagTAtCga- ; cor=; Ncor= a 0 0 0 6 4 3 0 1 10 4 14 2 2 15 1 0 1 15 0 11 1 2 12 4 0 2 10 0 c 0 0 0 4 5 4 14 1 4 0 1 11 3 1 1 16 0 0 1 0 4 1 1 0 12 4 1 0 g 0 0 0 3 4 2 1 15 0 1 1 4 0 1 0 0 16 1 1 2 10 2 0 4 2 11 3 0 t 0 0 0 4 4 8 2 0 3 12 1 0 12 0 15 1 0 1 15 4 2 12 4 9 3 0 3 0
dyads_m7_shift3 (dyads_m7)				; oligos_7nt_mkv2_m1 versus dyads_m7; m=5/10; ncol2=24; w=-1; offset=-1; strand=D; shift=3; score=0.866355; ---wswCGATAsTATCGATwstwdYrw- ; cor=; Ncor= a 0 0 0 5 2 3 0 2 9 1 11 0 1 11 1 0 0 10 1 7 0 1 8 3 0 3 6 0 c 0 0 0 1 4 2 11 0 2 0 1 5 0 0 1 12 0 0 1 1 5 2 0 0 9 0 0 0 g 0 0 0 2 4 0 0 10 0 0 0 7 0 1 0 0 12 1 1 1 6 2 0 3 0 8 1 0 t 0 0 0 4 2 7 1 0 1 11 0 0 11 0 10 0 0 1 9 3 1 7 4 6 3 1 5 0
oligos_6nt_mkv2_m2_shift8 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=6/10; ncol2=21; w=0; offset=4; strand=D; shift=8; score=0.688257; --------swwmyaTCGATAsTATCGAt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 c 0 0 0 0 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 g 0 0 0 0 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 t 0 0 0 0 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11
oligos_7nt_mkv2_m4_shift6 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=7/10; ncol2=24; w=0; offset=2; strand=D; shift=6; score=0.680504; ------yvsawmyatCGATAsTATCGAt ; cor=; Ncor= a 0 0 0 0 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 c 0 0 0 0 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 g 0 0 0 0 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 t 0 0 0 0 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13
oligos_7nt_mkv2_m2_rc_shift1 (oligos_7nt_mkv2_m2_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m2_rc; m=8/10; ncol2=24; w=-3; offset=-3; strand=R; shift=1; score=0.668967; -wyhrTCGATASTATCGAyrktwby--- ; cor=; Ncor= a 0 6 3 5 9 2 1 2 16 0 18 1 2 17 1 0 1 14 1 5 3 4 5 2 2 0 0 0 c 0 4 8 7 2 1 15 0 1 1 0 13 0 1 1 19 0 1 5 4 2 3 1 6 8 0 0 0 g 0 4 3 2 5 2 1 17 1 1 1 5 0 0 0 0 18 3 2 8 7 1 2 6 3 0 0 0 t 0 5 5 5 3 14 2 0 1 17 0 0 17 1 17 0 0 1 11 2 7 11 11 5 6 0 0 0
dyads_m2_rc_shift0 (dyads_m2_rc)				; oligos_7nt_mkv2_m1 versus dyads_m2_rc; m=9/10; ncol2=24; w=-4; offset=-4; strand=R; shift=0; score=0.590481; ayhyaTCGATAsTATCGAyvdtts---- ; cor=; Ncor= a 8 3 4 3 10 0 1 1 15 0 16 0 1 13 1 0 1 12 1 4 4 3 3 2 0 0 0 0 c 2 4 6 5 0 1 15 0 0 0 0 10 0 2 1 16 0 1 4 4 1 3 3 5 0 0 0 0 g 3 3 2 3 3 2 0 15 0 1 0 6 0 0 0 0 15 2 2 6 6 3 2 6 0 0 0 0 t 3 6 4 5 3 13 0 0 1 15 0 0 15 1 14 0 0 1 9 2 5 7 8 3 0 0 0 0
positions_6nt_m1_shift12 (positions_6nt_m1)				; oligos_7nt_mkv2_m1 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=8; strand=D; shift=12; score=0.41602; ------------haTCGATAGyw----- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=24; shift=3; ncol=27; ---rvwamyrTCGATASTATCGAydrw ; Alignment reference a 0 0 0 6 5 11 11 7 2 11 1 0 0 17 1 17 0 0 17 1 0 2 14 3 5 5 5 c 0 0 0 3 6 2 1 7 8 2 3 18 0 0 0 0 5 1 1 1 17 1 2 5 2 3 4 g 0 0 0 8 6 1 3 2 4 5 1 0 19 1 1 0 13 0 1 1 0 15 1 2 7 8 4 t 0 0 0 2 2 5 4 3 5 1 14 1 0 1 17 2 1 18 0 16 2 1 2 9 5 3 6
oligos_7nt_mkv2_m2_shift3 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/10; ncol2=24; w=0; offset=0; strand=D; shift=3; score= 1; ---rvwamyrTCGATASTATCGAydrw ; cor=; Ncor= a 0 0 0 6 5 11 11 7 2 11 1 0 0 17 1 17 0 0 17 1 0 2 14 3 5 5 5 c 0 0 0 3 6 2 1 7 8 2 3 18 0 0 0 0 5 1 1 1 17 1 2 5 2 3 4 g 0 0 0 8 6 1 3 2 4 5 1 0 19 1 1 0 13 0 1 1 0 15 1 2 7 8 4 t 0 0 0 2 2 5 4 3 5 1 14 1 0 1 17 2 1 18 0 16 2 1 2 9 5 3 6
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m4; m=2/10; ncol2=24; w=-1; offset=-1; strand=D; shift=2; score=0.904547; --yvsawmyatCGATAsTATCGAtwg- ; cor=; Ncor= a 0 0 4 6 4 13 10 7 4 12 2 0 1 21 1 22 0 1 20 1 0 1 17 2 7 5 0 c 0 0 7 6 7 4 4 8 9 4 5 23 0 0 0 0 7 1 1 2 21 1 2 5 5 3 0 g 0 0 4 8 8 3 3 4 4 5 1 0 22 1 1 0 15 0 2 0 0 20 2 3 5 12 0 t 0 0 8 3 4 3 6 4 6 2 15 0 0 1 21 1 1 21 0 20 2 1 2 13 6 3 0
dyads_m2_shift4 (dyads_m2)				; oligos_7nt_mkv2_m2 versus dyads_m2; m=3/10; ncol2=24; w=0; offset=1; strand=D; shift=4; score=0.90157; ----saahbrTCGATAsTATCGAtrdr ; cor=; Ncor= a 0 0 0 0 3 8 7 5 2 9 1 0 0 14 1 15 0 0 15 1 0 0 13 3 5 4 6 c 0 0 0 0 6 2 3 6 6 2 2 15 0 0 0 0 6 0 1 0 15 0 2 3 3 2 3 g 0 0 0 0 5 3 3 1 4 4 1 0 16 1 2 0 10 0 0 0 0 15 1 0 5 6 4 t 0 0 0 0 2 3 3 4 4 1 12 1 0 1 13 1 0 16 0 15 1 1 0 10 3 4 3
oligos_6nt_mkv2_m2_shift4 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=4/10; ncol2=21; w=0; offset=1; strand=D; shift=4; score=0.859793; ----swwmyaTCGATAsTATCGAth-- ; cor=; Ncor= a 0 0 0 0 4 10 10 6 4 13 2 0 1 22 0 21 1 0 21 1 0 1 16 4 6 0 0 c 0 0 0 0 7 4 4 8 8 2 4 22 0 0 0 0 7 1 2 0 22 1 3 5 6 0 0 g 0 0 0 0 7 3 3 4 4 5 1 0 22 0 2 0 14 0 0 1 0 21 2 3 5 0 0 t 0 0 0 0 5 6 6 5 7 3 16 1 0 1 21 2 1 22 0 21 1 0 2 11 6 0 0
dyads_m7_rc_shift1 (dyads_m7_rc)				; oligos_7nt_mkv2_m2 versus dyads_m7_rc; m=5/10; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.753248; -wyRhwaswATCGATAsTATCGwsw-- ; cor=; Ncor= a 0 5 1 3 6 4 7 1 3 9 1 0 0 10 0 11 0 0 11 1 0 1 7 2 4 0 0 c 0 1 8 0 3 0 2 6 1 1 1 12 0 0 1 0 7 0 0 0 10 0 0 4 2 0 0 g 0 0 0 9 0 0 2 5 1 1 0 0 12 1 0 0 5 1 0 2 0 11 2 4 1 0 0 t 0 6 3 0 3 8 1 0 7 1 10 0 0 1 11 1 0 11 1 9 2 0 3 2 5 0 0
oligos_7nt_mkv2_m5_rc_shift1 (oligos_7nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m5_rc; m=6/10; ncol2=24; w=-2; offset=-2; strand=R; shift=1; score=0.740443; -tcGaTActATCGATAgTAtCGagt-- ; cor=; Ncor= a 0 3 0 3 9 4 12 2 4 15 1 0 1 15 0 12 0 1 12 3 0 2 8 4 4 0 0 c 0 3 11 2 4 0 2 10 2 1 1 16 0 0 1 0 4 1 1 0 15 1 2 4 3 0 0 g 0 1 4 12 0 1 1 4 0 1 0 0 16 1 1 3 11 1 0 4 1 14 4 5 4 0 0 t 0 10 2 0 4 12 2 1 11 0 15 1 0 1 15 2 2 14 4 10 1 0 3 4 6 0 0
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=7/10; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.668967; stCGmTActATCGATagTAkCGas--- ; cor=; Ncor= a 3 3 0 2 10 4 14 2 4 16 1 0 1 16 0 11 0 1 13 3 0 2 10 4 0 0 0 c 5 3 13 2 5 0 2 12 3 1 1 17 0 0 1 0 4 1 1 0 14 3 2 6 0 0 0 g 6 2 3 14 0 1 1 4 0 1 0 0 17 1 1 3 12 2 0 5 2 13 3 5 0 0 0 t 4 10 2 0 3 13 1 0 11 0 16 1 0 1 16 4 2 14 4 10 2 0 3 3 0 0 0
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m1; m=8/10; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.662242; kyCGmTACwATCGATwGTAkCGrm--- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 0 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 0 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 0 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0 0 0
dyads_m1_shift0 (dyads_m1)				; oligos_7nt_mkv2_m2 versus dyads_m1; m=9/10; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.662242; kyCGmTACwATCGATwGTAkCGrm--- ; cor=; Ncor= a 4 4 0 4 13 5 16 2 6 19 1 0 1 19 1 13 0 1 16 3 0 2 10 7 0 0 0 c 5 6 17 2 6 0 3 15 3 1 2 20 1 0 1 0 5 2 1 0 16 3 2 6 0 0 0 g 6 2 3 16 0 1 2 5 0 1 0 1 20 2 1 3 15 3 0 6 2 17 6 5 0 0 0 t 7 10 2 0 3 16 1 0 13 1 19 1 0 1 19 6 2 16 5 13 4 0 4 4 0 0 0
positions_6nt_m1_shift8 (positions_6nt_m1)				; oligos_7nt_mkv2_m2 versus positions_6nt_m1; m=10/10; ncol2=11; w=0; offset=5; strand=D; shift=8; score=0.413795; --------haTCGATAGyw-------- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 25 45 5 2 0 85 4 74 3 11 31 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 24 11 5 84 1 2 2 0 12 27 15 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 14 16 4 1 86 0 3 8 69 12 14 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 25 16 74 1 1 1 79 6 4 38 28 0 0 0 0 0 0 0 0