One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.181428_2026-04-21.181428_T3sFyL/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.181428_2026-04-21.181428_T3sFyL/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; wvGATCGChd ; Alignment reference a 12 12 0 35 0 0 0 0 12 10 c 7 10 0 0 0 37 0 35 12 5 g 8 10 37 2 0 0 35 0 3 11 t 10 5 0 0 37 0 2 2 10 11

oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; wvGATCGChd ; cor=; Ncor= a 12 12 0 35 0 0 0 0 12 10 c 7 10 0 0 0 37 0 35 12 5 g 8 10 37 2 0 0 35 0 3 11 t 10 5 0 0 37 0 2 2 10 11

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; scAGCTGCAGct ; Alignment reference a 9 12 41 3 2 5 0 2 44 2 6 12 c 15 25 3 1 45 1 2 46 1 0 23 12 g 14 4 5 44 1 2 46 1 0 45 9 12 t 11 8 0 1 1 41 1 0 4 2 11 13

oligos_8nt_mkv2_m5_shift0 (oligos_8nt_mkv2_m5)
; oligos_8nt_mkv2_m5 versus oligos_8nt_mkv2_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; scAGCTGCAGct ; cor=; Ncor= a 9 12 41 3 2 5 0 2 44 2 6 12 c 15 25 3 1 45 1 2 46 1 0 23 12 g 14 4 5 44 1 2 46 1 0 45 9 12 t 11 8 0 1 1 41 1 0 4 2 11 13

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; cyTCCGCCGGmn ; Alignment reference a 9 8 3 0 0 1 0 0 2 4 10 10 c 17 13 1 38 38 1 37 36 0 1 19 10 g 9 6 3 1 2 35 3 0 36 33 7 10 t 5 13 33 1 0 3 0 4 2 2 4 10

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; cyTCCGCCGGmn ; cor=; Ncor= a 9 8 3 0 0 1 0 0 2 4 10 10 c 17 13 1 38 38 1 37 36 0 1 19 10 g 9 6 3 1 2 35 3 0 36 33 7 10 t 5 13 33 1 0 3 0 4 2 2 4 10

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m3; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.760215; -ywCCGCCGds- ; cor=; Ncor= a 0 10 17 1 0 5 4 0 0 17 12 0 c 0 21 12 54 52 2 49 56 1 6 19 0 g 0 7 8 0 2 46 0 0 52 18 14 0 t 0 18 19 1 2 3 3 0 3 15 11 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=2; ncol=13; --rrAAGGGGGgk ; Alignment reference a 0 0 22 28 72 66 10 4 3 2 3 16 16 c 0 0 18 14 1 1 2 3 3 2 0 17 16 g 0 0 20 30 0 3 55 60 60 68 67 22 21 t 0 0 13 1 0 3 6 6 7 1 3 18 20

oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --rrAAGGGGGgk ; cor=; Ncor= a 0 0 22 28 72 66 10 4 3 2 3 16 16 c 0 0 18 14 1 1 2 3 3 2 0 17 16 g 0 0 20 30 0 3 55 60 60 68 67 22 21 t 0 0 13 1 0 3 6 6 7 1 3 18 20

oligos_8nt_mkv2_m3_shift0 (oligos_8nt_mkv2_m3)
; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m3; m=2/3; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.790693; rarAAAGGGGGrb ; cor=; Ncor= a 14 15 11 38 38 34 5 2 3 1 2 16 8 c 5 10 9 1 0 1 1 3 0 0 0 10 11 g 14 10 20 4 5 7 34 36 37 41 39 11 12 t 10 8 3 0 0 1 3 2 3 1 2 6 12

oligos_6nt_mkv2_m4_shift2 (oligos_6nt_mkv2_m4)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.652575; --mrAAGGTGag- ; cor=; Ncor= a 0 0 12 12 33 33 0 0 0 0 14 5 0 c 0 0 11 7 0 1 0 0 0 0 6 8 0 g 0 0 4 10 0 0 34 34 0 34 8 14 0 t 0 0 7 5 1 0 0 0 34 0 6 7 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m1_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1)
; oligos_8nt_mkv2_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -rmAACAACAAha ; Alignment reference a 0 38 21 77 72 5 79 76 8 80 82 22 41 c 0 11 26 2 3 70 2 1 68 1 1 26 12 g 0 21 20 3 9 4 3 3 4 1 0 13 14 t 0 14 17 2 0 5 0 4 4 2 1 23 17

oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1)
; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -rmAACAACAAha ; cor=; Ncor= a 0 38 21 77 72 5 79 76 8 80 82 22 41 c 0 11 26 2 3 70 2 1 68 1 1 26 12 g 0 21 20 3 9 4 3 3 4 1 0 13 14 t 0 14 17 2 0 5 0 4 4 2 1 23 17

oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3)
; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=2/4; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.875409; --saACAACAAsw ; cor=; Ncor= a 0 0 17 34 65 0 61 60 0 59 66 16 23 c 0 0 21 11 2 65 2 1 67 3 2 22 12 g 0 0 22 10 2 1 6 0 1 3 1 18 14 t 0 0 10 15 1 4 1 9 2 5 1 14 21

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=3/4; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.619681; raAAACAAAAww- ; cor=; Ncor= a 45 48 100 109 108 1 107 109 113 102 42 45 0 c 25 16 9 1 4 99 5 1 2 3 20 19 0 g 30 28 4 1 2 9 4 6 1 5 20 17 0 t 19 27 6 8 5 10 3 3 3 9 37 38 0

oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1)
; oligos_8nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=4/4; ncol2=12; w=0; offset=2; strand=D; shift=3; score=0.559374; ---raCAACAAAT ; cor=; Ncor= a 0 0 0 22 23 10 65 66 2 68 66 61 9 c 0 0 0 15 16 50 1 2 63 1 1 3 2 g 0 0 0 22 16 4 0 0 1 1 2 3 2 t 0 0 0 11 15 6 4 2 4 0 1 3 57

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --raCAACAAATwr ; Alignment reference a 0 0 22 23 10 65 66 2 68 66 61 9 20 18 c 0 0 15 16 50 1 2 63 1 1 3 2 11 16 g 0 0 22 16 4 0 0 1 1 2 3 2 13 19 t 0 0 11 15 6 4 2 4 0 1 3 57 26 17

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --raCAACAAATwr ; cor=; Ncor= a 0 0 22 23 10 65 66 2 68 66 61 9 20 18 c 0 0 15 16 50 1 2 63 1 1 3 2 11 16 g 0 0 22 16 4 0 0 1 1 2 3 2 13 19 t 0 0 11 15 6 4 2 4 0 1 3 57 26 17

oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.768851; --raAAACAAAAww ; cor=; Ncor= a 0 0 45 48 100 109 108 1 107 109 113 102 42 45 c 0 0 25 16 9 1 4 99 5 1 2 3 20 19 g 0 0 30 28 4 1 2 9 4 6 1 5 20 17 t 0 0 19 27 6 8 5 10 3 3 3 9 37 38

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=3/4; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score=0.626934; -saACAACAAsw-- ; cor=; Ncor= a 0 17 34 65 0 61 60 0 59 66 16 23 0 0 c 0 21 11 2 65 2 1 67 3 2 22 12 0 0 g 0 22 10 2 1 6 0 1 3 1 18 14 0 0 t 0 10 15 1 4 1 9 2 5 1 14 21 0 0

oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m1; m=4/4; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.559374; rmAACAACAAha-- ; cor=; Ncor= a 38 21 77 72 5 79 76 8 80 82 22 41 0 0 c 11 26 2 3 70 2 1 68 1 1 26 12 0 0 g 21 20 3 9 4 3 3 4 1 0 13 14 0 0 t 14 17 2 0 5 0 4 4 2 1 23 17 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --wbCTCCTCCwb ; Alignment reference a 0 0 31 19 2 3 1 2 4 0 6 29 16 c 0 0 20 30 99 1 95 100 2 97 98 24 33 g 0 0 24 31 6 2 6 5 7 8 5 27 36 t 0 0 39 34 7 108 12 7 101 9 5 34 29

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --wbCTCCTCCwb ; cor=; Ncor= a 0 0 31 19 2 3 1 2 4 0 6 29 16 c 0 0 20 30 99 1 95 100 2 97 98 24 33 g 0 0 24 31 6 2 6 5 7 8 5 27 36 t 0 0 39 34 7 108 12 7 101 9 5 34 29

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.868515; -mwCCTCCTCCyb ; cor=; Ncor= a 0 11 10 4 0 0 0 1 2 0 0 6 3 c 0 15 5 30 34 0 33 34 0 33 33 10 10 g 0 7 6 3 1 0 2 0 3 2 2 9 12 t 0 4 16 0 2 37 2 2 32 2 2 12 12

oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m2; m=3/3; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.801005; cmtCCTCCTCCyb ; cor=; Ncor= a 10 12 10 6 0 0 0 1 2 0 0 7 4 c 13 18 5 32 35 0 37 37 0 37 35 12 11 g 9 7 6 3 2 0 2 1 3 2 2 9 13 t 9 4 20 0 4 41 2 2 36 2 4 13 13

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=12; shift=1; ncol=13; -mwCCTCCTCCyb ; Alignment reference a 0 11 10 4 0 0 0 1 2 0 0 6 3 c 0 15 5 30 34 0 33 34 0 33 33 10 10 g 0 7 6 3 1 0 2 0 3 2 2 9 12 t 0 4 16 0 2 37 2 2 32 2 2 12 12

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -mwCCTCCTCCyb ; cor=; Ncor= a 0 11 10 4 0 0 0 1 2 0 0 6 3 c 0 15 5 30 34 0 33 34 0 33 33 10 10 g 0 7 6 3 1 0 2 0 3 2 2 9 12 t 0 4 16 0 2 37 2 2 32 2 2 12 12

oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m2; m=2/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.921058; cmtCCTCCTCCyb ; cor=; Ncor= a 10 12 10 6 0 0 0 1 2 0 0 7 4 c 13 18 5 32 35 0 37 37 0 37 35 12 11 g 9 7 6 3 2 0 2 1 3 2 2 9 13 t 9 4 20 0 4 41 2 2 36 2 4 13 13

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.868515; --wbCTCCTCCwb ; cor=; Ncor= a 0 0 31 19 2 3 1 2 4 0 6 29 16 c 0 0 20 30 99 1 95 100 2 97 98 24 33 g 0 0 24 31 6 2 6 5 7 8 5 27 36 t 0 0 39 34 7 108 12 7 101 9 5 34 29

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2)
; oligos_8nt_mkv2_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; cmtCCTCCTCCyb ; Alignment reference a 10 12 10 6 0 0 0 1 2 0 0 7 4 c 13 18 5 32 35 0 37 37 0 37 35 12 11 g 9 7 6 3 2 0 2 1 3 2 2 9 13 t 9 4 20 0 4 41 2 2 36 2 4 13 13

oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2)
; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m2; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; cmtCCTCCTCCyb ; cor=; Ncor= a 10 12 10 6 0 0 0 1 2 0 0 7 4 c 13 18 5 32 35 0 37 37 0 37 35 12 11 g 9 7 6 3 2 0 2 1 3 2 2 9 13 t 9 4 20 0 4 41 2 2 36 2 4 13 13

oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)
; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.921058; -mwCCTCCTCCyb ; cor=; Ncor= a 0 11 10 4 0 0 0 1 2 0 0 6 3 c 0 15 5 30 34 0 33 34 0 33 33 10 10 g 0 7 6 3 1 0 2 0 3 2 2 9 12 t 0 4 16 0 2 37 2 2 32 2 2 12 12

oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)
; oligos_8nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=3/3; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.801005; --wbCTCCTCCwb ; cor=; Ncor= a 0 0 31 19 2 3 1 2 4 0 6 29 16 c 0 0 20 30 99 1 95 100 2 97 98 24 33 g 0 0 24 31 6 2 6 5 7 8 5 27 36 t 0 0 39 34 7 108 12 7 101 9 5 34 29

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m3_shift0 (oligos_8nt_mkv2_m3)
; oligos_8nt_mkv2_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; rarAAAGGGGGrb ; Alignment reference a 14 15 11 38 38 34 5 2 3 1 2 16 8 c 5 10 9 1 0 1 1 3 0 0 0 10 11 g 14 10 20 4 5 7 34 36 37 41 39 11 12 t 10 8 3 0 0 1 3 2 3 1 2 6 12

oligos_8nt_mkv2_m3_shift0 (oligos_8nt_mkv2_m3)
; oligos_8nt_mkv2_m3 versus oligos_8nt_mkv2_m3; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; rarAAAGGGGGrb ; cor=; Ncor= a 14 15 11 38 38 34 5 2 3 1 2 16 8 c 5 10 9 1 0 1 1 3 0 0 0 10 11 g 14 10 20 4 5 7 34 36 37 41 39 11 12 t 10 8 3 0 0 1 3 2 3 1 2 6 12

oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1)
; oligos_8nt_mkv2_m3 versus oligos_7nt_mkv2_m1; m=2/2; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.790693; --rrAAGGGGGgk ; cor=; Ncor= a 0 0 22 28 72 66 10 4 3 2 3 16 16 c 0 0 18 14 1 1 2 3 3 2 0 17 16 g 0 0 20 30 0 3 55 60 60 68 67 22 21 t 0 0 13 1 0 3 6 6 7 1 3 18 20

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -saACAACAAsw ; Alignment reference a 0 17 34 65 0 61 60 0 59 66 16 23 c 0 21 11 2 65 2 1 67 3 2 22 12 g 0 22 10 2 1 6 0 1 3 1 18 14 t 0 10 15 1 4 1 9 2 5 1 14 21

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -saACAACAAsw ; cor=; Ncor= a 0 17 34 65 0 61 60 0 59 66 16 23 c 0 21 11 2 65 2 1 67 3 2 22 12 g 0 22 10 2 1 6 0 1 3 1 18 14 t 0 10 15 1 4 1 9 2 5 1 14 21

oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)
; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m1; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.875409; rmAACAACAAha ; cor=; Ncor= a 38 21 77 72 5 79 76 8 80 82 22 41 c 11 26 2 3 70 2 1 68 1 1 26 12 g 21 20 3 9 4 3 3 4 1 0 13 14 t 14 17 2 0 5 0 4 4 2 1 23 17

oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=3/3; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.626934; --raCAACAAAT ; cor=; Ncor= a 0 0 22 23 10 65 66 2 68 66 61 9 c 0 0 15 16 50 1 2 63 1 1 3 2 g 0 0 22 16 4 0 0 1 1 2 3 2 t 0 0 11 15 6 4 2 4 0 1 3 57

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -ywCCGCCGds ; Alignment reference a 0 10 17 1 0 5 4 0 0 17 12 c 0 21 12 54 52 2 49 56 1 6 19 g 0 7 8 0 2 46 0 0 52 18 14 t 0 18 19 1 2 3 3 0 3 15 11

oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -ywCCGCCGds ; cor=; Ncor= a 0 10 17 1 0 5 4 0 0 17 12 c 0 21 12 54 52 2 49 56 1 6 19 g 0 7 8 0 2 46 0 0 52 18 14 t 0 18 19 1 2 3 3 0 3 15 11

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m3 versus oligos_7nt_mkv2_m5; m=2/2; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.760215; cyTCCGCCGGm ; cor=; Ncor= a 9 8 3 0 0 1 0 0 2 4 10 c 17 13 1 38 38 1 37 36 0 1 19 g 9 6 3 1 2 35 3 0 36 33 7 t 5 13 33 1 0 3 0 4 2 2 4

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; mrAAGGTGag ; Alignment reference a 12 12 33 33 0 0 0 0 14 5 c 11 7 0 1 0 0 0 0 6 8 g 4 10 0 0 34 34 0 34 8 14 t 7 5 1 0 0 0 34 0 6 7

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; mrAAGGTGag ; cor=; Ncor= a 12 12 33 33 0 0 0 0 14 5 c 11 7 0 1 0 0 0 0 6 8 g 4 10 0 0 34 34 0 34 8 14 t 7 5 1 0 0 0 34 0 6 7

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.652575; rrAAGGGGGg ; cor=; Ncor= a 22 28 72 66 10 4 3 2 3 16 c 18 14 1 1 2 3 3 2 0 17 g 20 30 0 3 55 60 60 68 67 22 t 13 1 0 3 6 6 7 1 3 18

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; raAAACAAAAww ; Alignment reference a 45 48 100 109 108 1 107 109 113 102 42 45 c 25 16 9 1 4 99 5 1 2 3 20 19 g 30 28 4 1 2 9 4 6 1 5 20 17 t 19 27 6 8 5 10 3 3 3 9 37 38

oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; raAAACAAAAww ; cor=; Ncor= a 45 48 100 109 108 1 107 109 113 102 42 45 c 25 16 9 1 4 99 5 1 2 3 20 19 g 30 28 4 1 2 9 4 6 1 5 20 17 t 19 27 6 8 5 10 3 3 3 9 37 38

oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.768851; raCAACAAATwr ; cor=; Ncor= a 22 23 10 65 66 2 68 66 61 9 20 18 c 15 16 50 1 2 63 1 1 3 2 11 16 g 22 16 4 0 0 1 1 2 3 2 13 19 t 11 15 6 4 2 4 0 1 3 57 26 17

oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m1; m=3/3; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.619681; -rmAACAACAAh ; cor=; Ncor= a 0 38 21 77 72 5 79 76 8 80 82 22 c 0 11 26 2 3 70 2 1 68 1 1 26 g 0 21 20 3 9 4 3 3 4 1 0 13 t 0 14 17 2 0 5 0 4 4 2 1 23

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m4_shift0 (oligos_8nt_mkv2_m4)
; oligos_8nt_mkv2_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; acaCACACACAya ; Alignment reference a 46 19 50 3 81 0 76 1 81 2 80 12 46 c 15 46 7 83 1 85 5 85 3 85 5 50 11 g 17 10 22 1 4 3 3 1 2 1 2 5 17 t 14 17 13 5 6 4 8 5 6 4 5 25 18

oligos_8nt_mkv2_m4_shift0 (oligos_8nt_mkv2_m4)
; oligos_8nt_mkv2_m4 versus oligos_8nt_mkv2_m4; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; acaCACACACAya ; cor=; Ncor= a 46 19 50 3 81 0 76 1 81 2 80 12 46 c 15 46 7 83 1 85 5 85 3 85 5 50 11 g 17 10 22 1 4 3 3 1 2 1 2 5 17 t 14 17 13 5 6 4 8 5 6 4 5 25 18

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=2; ncol=13; --rrAAGGGGGgk ; Alignment reference a 0 0 22 28 72 66 10 4 3 2 3 16 16 c 0 0 18 14 1 1 2 3 3 2 0 17 16 g 0 0 20 30 0 3 55 60 60 68 67 22 21 t 0 0 13 1 0 3 6 6 7 1 3 18 20
oligos_7nt_mkv2_m1_shift2 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --rrAAGGGGGgk ; cor=; Ncor= a 0 0 22 28 72 66 10 4 3 2 3 16 16 c 0 0 18 14 1 1 2 3 3 2 0 17 16 g 0 0 20 30 0 3 55 60 60 68 67 22 21 t 0 0 13 1 0 3 6 6 7 1 3 18 20
oligos_8nt_mkv2_m3_shift0 (oligos_8nt_mkv2_m3)				; oligos_7nt_mkv2_m1 versus oligos_8nt_mkv2_m3; m=2/3; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.790693; rarAAAGGGGGrb ; cor=; Ncor= a 14 15 11 38 38 34 5 2 3 1 2 16 8 c 5 10 9 1 0 1 1 3 0 0 0 10 11 g 14 10 20 4 5 7 34 36 37 41 39 11 12 t 10 8 3 0 0 1 3 2 3 1 2 6 12
oligos_6nt_mkv2_m4_shift2 (oligos_6nt_mkv2_m4)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m4; m=3/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.652575; --mrAAGGTGag- ; cor=; Ncor= a 0 0 12 12 33 33 0 0 0 0 14 5 0 c 0 0 11 7 0 1 0 0 0 0 6 8 0 g 0 0 4 10 0 0 34 34 0 34 8 14 0 t 0 0 7 5 1 0 0 0 34 0 6 7 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1)				; oligos_8nt_mkv2_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -rmAACAACAAha ; Alignment reference a 0 38 21 77 72 5 79 76 8 80 82 22 41 c 0 11 26 2 3 70 2 1 68 1 1 26 12 g 0 21 20 3 9 4 3 3 4 1 0 13 14 t 0 14 17 2 0 5 0 4 4 2 1 23 17
oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1)				; oligos_8nt_mkv2_m1 versus oligos_8nt_mkv2_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -rmAACAACAAha ; cor=; Ncor= a 0 38 21 77 72 5 79 76 8 80 82 22 41 c 0 11 26 2 3 70 2 1 68 1 1 26 12 g 0 21 20 3 9 4 3 3 4 1 0 13 14 t 0 14 17 2 0 5 0 4 4 2 1 23 17
oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3)				; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=2/4; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.875409; --saACAACAAsw ; cor=; Ncor= a 0 0 17 34 65 0 61 60 0 59 66 16 23 c 0 0 21 11 2 65 2 1 67 3 2 22 12 g 0 0 22 10 2 1 6 0 1 3 1 18 14 t 0 0 10 15 1 4 1 9 2 5 1 14 21
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_8nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=3/4; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.619681; raAAACAAAAww- ; cor=; Ncor= a 45 48 100 109 108 1 107 109 113 102 42 45 0 c 25 16 9 1 4 99 5 1 2 3 20 19 0 g 30 28 4 1 2 9 4 6 1 5 20 17 0 t 19 27 6 8 5 10 3 3 3 9 37 38 0
oligos_6nt_mkv2_m1_shift3 (oligos_6nt_mkv2_m1)				; oligos_8nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=4/4; ncol2=12; w=0; offset=2; strand=D; shift=3; score=0.559374; ---raCAACAAAT ; cor=; Ncor= a 0 0 0 22 23 10 65 66 2 68 66 61 9 c 0 0 0 15 16 50 1 2 63 1 1 3 2 g 0 0 0 22 16 4 0 0 1 1 2 3 2 t 0 0 0 11 15 6 4 2 4 0 1 3 57

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --raCAACAAATwr ; Alignment reference a 0 0 22 23 10 65 66 2 68 66 61 9 20 18 c 0 0 15 16 50 1 2 63 1 1 3 2 11 16 g 0 0 22 16 4 0 0 1 1 2 3 2 13 19 t 0 0 11 15 6 4 2 4 0 1 3 57 26 17
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --raCAACAAATwr ; cor=; Ncor= a 0 0 22 23 10 65 66 2 68 66 61 9 20 18 c 0 0 15 16 50 1 2 63 1 1 3 2 11 16 g 0 0 22 16 4 0 0 1 1 2 3 2 13 19 t 0 0 11 15 6 4 2 4 0 1 3 57 26 17
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=2/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score=0.768851; --raAAACAAAAww ; cor=; Ncor= a 0 0 45 48 100 109 108 1 107 109 113 102 42 45 c 0 0 25 16 9 1 4 99 5 1 2 3 20 19 g 0 0 30 28 4 1 2 9 4 6 1 5 20 17 t 0 0 19 27 6 8 5 10 3 3 3 9 37 38
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3; m=3/4; ncol2=11; w=-1; offset=-1; strand=D; shift=1; score=0.626934; -saACAACAAsw-- ; cor=; Ncor= a 0 17 34 65 0 61 60 0 59 66 16 23 0 0 c 0 21 11 2 65 2 1 67 3 2 22 12 0 0 g 0 22 10 2 1 6 0 1 3 1 18 14 0 0 t 0 10 15 1 4 1 9 2 5 1 14 21 0 0
oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_8nt_mkv2_m1; m=4/4; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.559374; rmAACAACAAha-- ; cor=; Ncor= a 38 21 77 72 5 79 76 8 80 82 22 41 0 0 c 11 26 2 3 70 2 1 68 1 1 26 12 0 0 g 21 20 3 9 4 3 3 4 1 0 13 14 0 0 t 14 17 2 0 5 0 4 4 2 1 23 17 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --wbCTCCTCCwb ; Alignment reference a 0 0 31 19 2 3 1 2 4 0 6 29 16 c 0 0 20 30 99 1 95 100 2 97 98 24 33 g 0 0 24 31 6 2 6 5 7 8 5 27 36 t 0 0 39 34 7 108 12 7 101 9 5 34 29
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --wbCTCCTCCwb ; cor=; Ncor= a 0 0 31 19 2 3 1 2 4 0 6 29 16 c 0 0 20 30 99 1 95 100 2 97 98 24 33 g 0 0 24 31 6 2 6 5 7 8 5 27 36 t 0 0 39 34 7 108 12 7 101 9 5 34 29
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.868515; -mwCCTCCTCCyb ; cor=; Ncor= a 0 11 10 4 0 0 0 1 2 0 0 6 3 c 0 15 5 30 34 0 33 34 0 33 33 10 10 g 0 7 6 3 1 0 2 0 3 2 2 9 12 t 0 4 16 0 2 37 2 2 32 2 2 12 12
oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_8nt_mkv2_m2; m=3/3; ncol2=13; w=-2; offset=-2; strand=D; shift=0; score=0.801005; cmtCCTCCTCCyb ; cor=; Ncor= a 10 12 10 6 0 0 0 1 2 0 0 7 4 c 13 18 5 32 35 0 37 37 0 37 35 12 11 g 9 7 6 3 2 0 2 1 3 2 2 9 13 t 9 4 20 0 4 41 2 2 36 2 4 13 13

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=12; shift=1; ncol=13; -mwCCTCCTCCyb ; Alignment reference a 0 11 10 4 0 0 0 1 2 0 0 6 3 c 0 15 5 30 34 0 33 34 0 33 33 10 10 g 0 7 6 3 1 0 2 0 3 2 2 9 12 t 0 4 16 0 2 37 2 2 32 2 2 12 12
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -mwCCTCCTCCyb ; cor=; Ncor= a 0 11 10 4 0 0 0 1 2 0 0 6 3 c 0 15 5 30 34 0 33 34 0 33 33 10 10 g 0 7 6 3 1 0 2 0 3 2 2 9 12 t 0 4 16 0 2 37 2 2 32 2 2 12 12
oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_8nt_mkv2_m2; m=2/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.921058; cmtCCTCCTCCyb ; cor=; Ncor= a 10 12 10 6 0 0 0 1 2 0 0 7 4 c 13 18 5 32 35 0 37 37 0 37 35 12 11 g 9 7 6 3 2 0 2 1 3 2 2 9 13 t 9 4 20 0 4 41 2 2 36 2 4 13 13
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=2; score=0.868515; --wbCTCCTCCwb ; cor=; Ncor= a 0 0 31 19 2 3 1 2 4 0 6 29 16 c 0 0 20 30 99 1 95 100 2 97 98 24 33 g 0 0 24 31 6 2 6 5 7 8 5 27 36 t 0 0 39 34 7 108 12 7 101 9 5 34 29

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2)				; oligos_8nt_mkv2_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; cmtCCTCCTCCyb ; Alignment reference a 10 12 10 6 0 0 0 1 2 0 0 7 4 c 13 18 5 32 35 0 37 37 0 37 35 12 11 g 9 7 6 3 2 0 2 1 3 2 2 9 13 t 9 4 20 0 4 41 2 2 36 2 4 13 13
oligos_8nt_mkv2_m2_shift0 (oligos_8nt_mkv2_m2)				; oligos_8nt_mkv2_m2 versus oligos_8nt_mkv2_m2; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; cmtCCTCCTCCyb ; cor=; Ncor= a 10 12 10 6 0 0 0 1 2 0 0 7 4 c 13 18 5 32 35 0 37 37 0 37 35 12 11 g 9 7 6 3 2 0 2 1 3 2 2 9 13 t 9 4 20 0 4 41 2 2 36 2 4 13 13
oligos_7nt_mkv2_m2_shift1 (oligos_7nt_mkv2_m2)				; oligos_8nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.921058; -mwCCTCCTCCyb ; cor=; Ncor= a 0 11 10 4 0 0 0 1 2 0 0 6 3 c 0 15 5 30 34 0 33 34 0 33 33 10 10 g 0 7 6 3 1 0 2 0 3 2 2 9 12 t 0 4 16 0 2 37 2 2 32 2 2 12 12
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2)				; oligos_8nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=3/3; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.801005; --wbCTCCTCCwb ; cor=; Ncor= a 0 0 31 19 2 3 1 2 4 0 6 29 16 c 0 0 20 30 99 1 95 100 2 97 98 24 33 g 0 0 24 31 6 2 6 5 7 8 5 27 36 t 0 0 39 34 7 108 12 7 101 9 5 34 29

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -saACAACAAsw ; Alignment reference a 0 17 34 65 0 61 60 0 59 66 16 23 c 0 21 11 2 65 2 1 67 3 2 22 12 g 0 22 10 2 1 6 0 1 3 1 18 14 t 0 10 15 1 4 1 9 2 5 1 14 21
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -saACAACAAsw ; cor=; Ncor= a 0 17 34 65 0 61 60 0 59 66 16 23 c 0 21 11 2 65 2 1 67 3 2 22 12 g 0 22 10 2 1 6 0 1 3 1 18 14 t 0 10 15 1 4 1 9 2 5 1 14 21
oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)				; oligos_7nt_mkv2_m3 versus oligos_8nt_mkv2_m1; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.875409; rmAACAACAAha ; cor=; Ncor= a 38 21 77 72 5 79 76 8 80 82 22 41 c 11 26 2 3 70 2 1 68 1 1 26 12 g 21 20 3 9 4 3 3 4 1 0 13 14 t 14 17 2 0 5 0 4 4 2 1 23 17
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=3/3; ncol2=12; w=0; offset=1; strand=D; shift=2; score=0.626934; --raCAACAAAT ; cor=; Ncor= a 0 0 22 23 10 65 66 2 68 66 61 9 c 0 0 15 16 50 1 2 63 1 1 3 2 g 0 0 22 16 4 0 0 1 1 2 3 2 t 0 0 11 15 6 4 2 4 0 1 3 57

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; raAAACAAAAww ; Alignment reference a 45 48 100 109 108 1 107 109 113 102 42 45 c 25 16 9 1 4 99 5 1 2 3 20 19 g 30 28 4 1 2 9 4 6 1 5 20 17 t 19 27 6 8 5 10 3 3 3 9 37 38
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; raAAACAAAAww ; cor=; Ncor= a 45 48 100 109 108 1 107 109 113 102 42 45 c 25 16 9 1 4 99 5 1 2 3 20 19 g 30 28 4 1 2 9 4 6 1 5 20 17 t 19 27 6 8 5 10 3 3 3 9 37 38
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.768851; raCAACAAATwr ; cor=; Ncor= a 22 23 10 65 66 2 68 66 61 9 20 18 c 15 16 50 1 2 63 1 1 3 2 11 16 g 22 16 4 0 0 1 1 2 3 2 13 19 t 11 15 6 4 2 4 0 1 3 57 26 17
oligos_8nt_mkv2_m1_shift1 (oligos_8nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_8nt_mkv2_m1; m=3/3; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.619681; -rmAACAACAAh ; cor=; Ncor= a 0 38 21 77 72 5 79 76 8 80 82 22 c 0 11 26 2 3 70 2 1 68 1 1 26 g 0 21 20 3 9 4 3 3 4 1 0 13 t 0 14 17 2 0 5 0 4 4 2 1 23