One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/03/26/peak-motifs.2025-03-26.185353_2025-03-26.185353_2AVZQp/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/2025/03/26/peak-motifs.2025-03-26.185353_2025-03-26.185353_2AVZQp/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=14; shift=1; ncol=15; -wwdCAGCAAAAAta ; Alignment reference a 0 25 29 24 2 80 6 2 71 76 66 78 65 13 34 c 0 12 10 5 77 0 3 79 1 5 2 2 3 11 12 g 0 12 15 26 2 1 72 0 2 1 0 0 0 13 17 t 0 33 28 27 1 1 1 1 8 0 14 2 14 45 19

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wwdCAGCAAAAAta ; cor=; Ncor= a 0 25 29 24 2 80 6 2 71 76 66 78 65 13 34 c 0 12 10 5 77 0 3 79 1 5 2 2 3 11 12 g 0 12 15 26 2 1 72 0 2 1 0 0 0 13 17 t 0 33 28 27 1 1 1 1 8 0 14 2 14 45 19

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=2/5; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.980762; -wwwCAGCAAAAAta ; cor=; Ncor= a 0 43 54 60 5 108 7 4 101 105 83 86 81 24 44 c 0 14 10 5 101 1 2 106 1 4 5 12 5 19 23 g 0 14 14 16 2 2 103 1 3 2 2 4 5 19 19 t 0 42 35 32 5 2 1 2 8 2 23 11 22 51 27

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m5; m=3/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.922632; wwawCAGCAAAAAta ; cor=; Ncor= a 25 26 41 22 2 79 4 2 67 72 64 77 67 12 34 c 12 11 7 5 74 0 2 75 2 4 1 0 1 10 16 g 16 13 13 11 2 0 73 1 1 1 0 1 0 14 14 t 27 30 19 42 2 1 1 2 10 3 15 2 12 44 16

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=4/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.914191; awawCAGCAAAAAta ; cor=; Ncor= a 34 28 49 48 4 80 3 1 73 78 70 79 69 16 38 c 14 10 5 4 73 1 1 84 2 4 1 2 1 14 19 g 17 14 11 11 2 1 81 0 3 2 0 1 4 14 12 t 21 34 21 23 7 4 1 1 8 2 15 4 12 42 17

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=5/5; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.774694; wwaACAGCAAwAat- ; cor=; Ncor= a 23 23 39 48 2 61 0 3 61 61 18 54 33 11 0 c 9 10 6 2 58 0 0 61 1 1 2 3 5 14 0 g 12 10 5 6 0 2 65 1 4 2 2 4 13 13 0 t 22 23 16 10 6 3 1 1 0 2 44 5 15 28 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 6 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=15; shift=0; ncol=15; wwawCAGCAAAAAta ; Alignment reference a 25 26 41 22 2 79 4 2 67 72 64 77 67 12 34 c 12 11 7 5 74 0 2 75 2 4 1 0 1 10 16 g 16 13 13 11 2 0 73 1 1 1 0 1 0 14 14 t 27 30 19 42 2 1 1 2 10 3 15 2 12 44 16

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; wwawCAGCAAAAAta ; cor=; Ncor= a 25 26 41 22 2 79 4 2 67 72 64 77 67 12 34 c 12 11 7 5 74 0 2 75 2 4 1 0 1 10 16 g 16 13 13 11 2 0 73 1 1 1 0 1 0 14 14 t 27 30 19 42 2 1 1 2 10 3 15 2 12 44 16

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.981691; awawCAGCAAAAAta ; cor=; Ncor= a 34 28 49 48 4 80 3 1 73 78 70 79 69 16 38 c 14 10 5 4 73 1 1 84 2 4 1 2 1 14 19 g 17 14 11 11 2 1 81 0 3 2 0 1 4 14 12 t 21 34 21 23 7 4 1 1 8 2 15 4 12 42 17

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m4; m=3/5; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.922632; -wwdCAGCAAAAAta ; cor=; Ncor= a 0 25 29 24 2 80 6 2 71 76 66 78 65 13 34 c 0 12 10 5 77 0 3 79 1 5 2 2 3 11 12 g 0 12 15 26 2 1 72 0 2 1 0 0 0 13 17 t 0 33 28 27 1 1 1 1 8 0 14 2 14 45 19

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=4/5; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.91279; -wwwCAGCAAAAAta ; cor=; Ncor= a 0 43 54 60 5 108 7 4 101 105 83 86 81 24 44 c 0 14 10 5 101 1 2 106 1 4 5 12 5 19 23 g 0 14 14 16 2 2 103 1 3 2 2 4 5 19 19 t 0 42 35 32 5 2 1 2 8 2 23 11 22 51 27

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m3_rc; m=5/5; ncol2=14; w=0; offset=0; strand=R; shift=0; score= 0.8345; wwaACAGCAAwAat- ; cor=; Ncor= a 23 23 39 48 2 61 0 3 61 61 18 54 33 11 0 c 9 10 6 2 58 0 0 61 1 1 2 3 5 14 0 g 12 10 5 6 0 2 65 1 4 2 2 4 13 13 0 t 22 23 16 10 6 3 1 1 0 2 44 5 15 28 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; wrCTGATAAtw ; Alignment reference a 22 29 2 0 4 61 2 68 58 17 26 c 14 12 66 1 1 2 4 0 6 14 4 g 8 18 3 1 67 4 4 3 4 15 17 t 28 13 1 70 0 5 62 1 4 26 25

oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wrCTGATAAtw ; cor=; Ncor= a 22 29 2 0 4 61 2 68 58 17 26 c 14 12 66 1 1 2 4 0 6 14 4 g 8 18 3 1 67 4 4 3 4 15 17 t 28 13 1 70 0 5 62 1 4 26 25

oligos_6nt_mkv2_m2_shift1 (oligos_6nt_mkv2_m2)
; oligos_7nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.84242; -wmTGATAAww ; cor=; Ncor= a 0 21 21 0 0 60 0 60 60 21 23 c 0 9 20 0 0 0 0 0 0 6 7 g 0 13 8 0 60 0 0 0 0 14 14 t 0 17 11 60 0 0 60 0 0 19 16

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; awawCAGCAAAAAta ; Alignment reference a 34 28 49 48 4 80 3 1 73 78 70 79 69 16 38 c 14 10 5 4 73 1 1 84 2 4 1 2 1 14 19 g 17 14 11 11 2 1 81 0 3 2 0 1 4 14 12 t 21 34 21 23 7 4 1 1 8 2 15 4 12 42 17

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; awawCAGCAAAAAta ; cor=; Ncor= a 34 28 49 48 4 80 3 1 73 78 70 79 69 16 38 c 14 10 5 4 73 1 1 84 2 4 1 2 1 14 19 g 17 14 11 11 2 1 81 0 3 2 0 1 4 14 12 t 21 34 21 23 7 4 1 1 8 2 15 4 12 42 17

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.981691; wwawCAGCAAAAAta ; cor=; Ncor= a 25 26 41 22 2 79 4 2 67 72 64 77 67 12 34 c 12 11 7 5 74 0 2 75 2 4 1 0 1 10 16 g 16 13 13 11 2 0 73 1 1 1 0 1 0 14 14 t 27 30 19 42 2 1 1 2 10 3 15 2 12 44 16

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=3/5; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.925761; -wwwCAGCAAAAAta ; cor=; Ncor= a 0 43 54 60 5 108 7 4 101 105 83 86 81 24 44 c 0 14 10 5 101 1 2 106 1 4 5 12 5 19 23 g 0 14 14 16 2 2 103 1 3 2 2 4 5 19 19 t 0 42 35 32 5 2 1 2 8 2 23 11 22 51 27

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=4/5; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.914191; -wwdCAGCAAAAAta ; cor=; Ncor= a 0 25 29 24 2 80 6 2 71 76 66 78 65 13 34 c 0 12 10 5 77 0 3 79 1 5 2 2 3 11 12 g 0 12 15 26 2 1 72 0 2 1 0 0 0 13 17 t 0 33 28 27 1 1 1 1 8 0 14 2 14 45 19

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=5/5; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.864997; wwaACAGCAAwAat- ; cor=; Ncor= a 23 23 39 48 2 61 0 3 61 61 18 54 33 11 0 c 9 10 6 2 58 0 0 61 1 1 2 3 5 14 0 g 12 10 5 6 0 2 65 1 4 2 2 4 13 13 0 t 22 23 16 10 6 3 1 1 0 2 44 5 15 28 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift1 ; 6 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=14; shift=1; ncol=15; -atTwTTGCTGTtww ; Alignment reference a 0 28 15 5 44 2 0 1 1 3 6 10 16 23 22 c 0 13 13 4 2 2 4 1 65 2 0 6 5 10 12 g 0 14 5 3 2 1 1 61 0 0 58 2 6 10 9 t 0 11 33 54 18 61 61 3 0 61 2 48 39 23 23

oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -atTwTTGCTGTtww ; cor=; Ncor= a 0 28 15 5 44 2 0 1 1 3 6 10 16 23 22 c 0 13 13 4 2 2 4 1 65 2 0 6 5 10 12 g 0 14 5 3 2 1 1 61 0 0 58 2 6 10 9 t 0 11 33 54 18 61 61 3 0 61 2 48 39 23 23

oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=2/5; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.864997; taTTTTTGCTGwtwt ; cor=; Ncor= a 17 42 12 4 15 2 8 1 1 4 7 23 21 34 21 c 12 14 4 1 0 2 3 0 81 1 2 11 11 14 17 g 19 14 1 2 1 4 2 84 1 1 73 4 5 10 14 t 38 16 69 79 70 78 73 1 3 80 4 48 49 28 34

oligos_7nt_mkv2_m5_rc_shift0 (oligos_7nt_mkv2_m5_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m5_rc; m=3/5; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score= 0.8345; taTTTTTGCTGwtww ; cor=; Ncor= a 16 44 12 2 15 3 10 2 1 1 2 42 19 30 27 c 14 14 0 1 0 1 1 1 73 0 2 11 13 13 16 g 16 10 1 0 1 4 2 75 2 0 74 5 7 11 12 t 34 12 67 77 64 72 67 2 4 79 2 22 41 26 25

oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)
; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=4/5; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.813052; taTTTTTGCTGwww- ; cor=; Ncor= a 27 51 22 11 23 2 8 2 1 2 5 32 35 42 0 c 19 19 5 4 2 2 3 1 103 2 2 16 14 14 0 g 23 19 5 12 5 4 1 106 2 1 101 5 10 14 0 t 44 24 81 86 83 105 101 4 7 108 5 60 54 43 0

oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)
; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=5/5; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.774694; taTTTTTGCTGhww- ; cor=; Ncor= a 19 45 14 2 14 0 8 1 1 1 1 27 28 33 0 c 17 13 0 0 0 1 2 0 72 1 2 26 15 12 0 g 12 11 3 2 2 5 1 79 3 0 77 5 10 12 0 t 34 13 65 78 66 76 71 2 6 80 2 24 29 25 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---wmTGATAAww ; Alignment reference a 0 0 0 21 21 0 0 60 0 60 60 21 23 c 0 0 0 9 20 0 0 0 0 0 0 6 7 g 0 0 0 13 8 0 60 0 0 0 0 14 14 t 0 0 0 17 11 60 0 0 60 0 0 19 16

oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---wmTGATAAww ; cor=; Ncor= a 0 0 0 21 21 0 0 60 0 60 60 21 23 c 0 0 0 9 20 0 0 0 0 0 0 6 7 g 0 0 0 13 8 0 60 0 0 0 0 14 14 t 0 0 0 17 11 60 0 0 60 0 0 19 16

oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)
; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=2; score=0.84242; --wrCTGATAAtw ; cor=; Ncor= a 0 0 22 29 2 0 4 61 2 68 58 17 26 c 0 0 14 12 66 1 1 2 4 0 6 14 4 g 0 0 8 18 3 1 67 4 4 3 4 15 17 t 0 0 28 13 1 70 0 5 62 1 4 26 25

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=3/3; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.453021; wwwAATGATrw-- ; cor=; Ncor= a 22 23 21 63 63 0 0 63 0 22 19 0 0 c 9 8 13 0 0 0 0 0 0 11 11 0 0 g 11 9 7 0 0 0 63 0 0 16 10 0 0 t 21 23 22 0 0 63 0 0 63 14 23 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -wwwCAGCAAAAAta ; Alignment reference a 0 43 54 60 5 108 7 4 101 105 83 86 81 24 44 c 0 14 10 5 101 1 2 106 1 4 5 12 5 19 23 g 0 14 14 16 2 2 103 1 3 2 2 4 5 19 19 t 0 42 35 32 5 2 1 2 8 2 23 11 22 51 27

oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wwwCAGCAAAAAta ; cor=; Ncor= a 0 43 54 60 5 108 7 4 101 105 83 86 81 24 44 c 0 14 10 5 101 1 2 106 1 4 5 12 5 19 23 g 0 14 14 16 2 2 103 1 3 2 2 4 5 19 19 t 0 42 35 32 5 2 1 2 8 2 23 11 22 51 27

oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=2/5; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.980762; -wwdCAGCAAAAAta ; cor=; Ncor= a 0 25 29 24 2 80 6 2 71 76 66 78 65 13 34 c 0 12 10 5 77 0 3 79 1 5 2 2 3 11 12 g 0 12 15 26 2 1 72 0 2 1 0 0 0 13 17 t 0 33 28 27 1 1 1 1 8 0 14 2 14 45 19

oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.925761; awawCAGCAAAAAta ; cor=; Ncor= a 34 28 49 48 4 80 3 1 73 78 70 79 69 16 38 c 14 10 5 4 73 1 1 84 2 4 1 2 1 14 19 g 17 14 11 11 2 1 81 0 3 2 0 1 4 14 12 t 21 34 21 23 7 4 1 1 8 2 15 4 12 42 17

oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=4/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.91279; wwawCAGCAAAAAta ; cor=; Ncor= a 25 26 41 22 2 79 4 2 67 72 64 77 67 12 34 c 12 11 7 5 74 0 2 75 2 4 1 0 1 10 16 g 16 13 13 11 2 0 73 1 1 1 0 1 0 14 14 t 27 30 19 42 2 1 1 2 10 3 15 2 12 44 16

oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)
; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=5/5; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.813052; wwaACAGCAAwAat- ; cor=; Ncor= a 23 23 39 48 2 61 0 3 61 61 18 54 33 11 0 c 9 10 6 2 58 0 0 61 1 1 2 3 5 14 0 g 12 10 5 6 0 2 65 1 4 2 2 4 13 13 0 t 22 23 16 10 6 3 1 1 0 2 44 5 15 28 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wwwAATGATrw ; Alignment reference a 22 23 21 63 63 0 0 63 0 22 19 c 9 8 13 0 0 0 0 0 0 11 11 g 11 9 7 0 0 0 63 0 0 16 10 t 21 23 22 0 0 63 0 0 63 14 23

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwwAATGATrw ; cor=; Ncor= a 22 23 21 63 63 0 0 63 0 22 19 c 9 8 13 0 0 0 0 0 0 11 11 g 11 9 7 0 0 0 63 0 0 16 10 t 21 23 22 0 0 63 0 0 63 14 23

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.698748; -gwAATAATra ; cor=; Ncor= a 0 19 26 79 79 0 79 79 0 32 35 c 0 19 17 0 0 0 0 0 0 9 16 g 0 24 8 0 0 0 0 0 0 22 15 t 0 17 28 0 0 79 0 0 79 16 13

oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)
; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m2; m=3/3; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.453021; ---wmTGATAA ; cor=; Ncor= a 0 0 0 21 21 0 0 60 0 60 60 c 0 0 0 9 20 0 0 0 0 0 0 g 0 0 0 13 8 0 60 0 0 0 0 t 0 0 0 17 11 60 0 0 60 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift0 ; 2 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; tkCTTCTCyd ; Alignment reference a 10 8 0 0 3 0 0 0 9 11 c 7 10 41 1 1 41 0 41 14 7 g 10 11 0 4 0 0 0 0 6 12 t 14 12 0 36 37 0 41 0 12 11

oligos_6nt_mkv2_m4_shift0 (oligos_6nt_mkv2_m4)
; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; tkCTTCTCyd ; cor=; Ncor= a 10 8 0 0 3 0 0 0 9 11 c 7 10 41 1 1 41 0 41 14 7 g 10 11 0 4 0 0 0 0 6 12 t 14 12 0 36 37 0 41 0 12 11

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -gwAATAATra ; Alignment reference a 0 19 26 79 79 0 79 79 0 32 35 c 0 19 17 0 0 0 0 0 0 9 16 g 0 24 8 0 0 0 0 0 0 22 15 t 0 17 28 0 0 79 0 0 79 16 13

oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -gwAATAATra ; cor=; Ncor= a 0 19 26 79 79 0 79 79 0 32 35 c 0 19 17 0 0 0 0 0 0 9 16 g 0 24 8 0 0 0 0 0 0 22 15 t 0 17 28 0 0 79 0 0 79 16 13

oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)
; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m3; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.698748; wwwAATGATrw ; cor=; Ncor= a 22 23 21 63 63 0 0 63 0 22 19 c 9 8 13 0 0 0 0 0 0 11 11 g 11 9 7 0 0 0 63 0 0 16 10 t 21 23 22 0 0 63 0 0 63 14 23

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=14; shift=1; ncol=15; -wwdCAGCAAAAAta ; Alignment reference a 0 25 29 24 2 80 6 2 71 76 66 78 65 13 34 c 0 12 10 5 77 0 3 79 1 5 2 2 3 11 12 g 0 12 15 26 2 1 72 0 2 1 0 0 0 13 17 t 0 33 28 27 1 1 1 1 8 0 14 2 14 45 19
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wwdCAGCAAAAAta ; cor=; Ncor= a 0 25 29 24 2 80 6 2 71 76 66 78 65 13 34 c 0 12 10 5 77 0 3 79 1 5 2 2 3 11 12 g 0 12 15 26 2 1 72 0 2 1 0 0 0 13 17 t 0 33 28 27 1 1 1 1 8 0 14 2 14 45 19
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m1; m=2/5; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.980762; -wwwCAGCAAAAAta ; cor=; Ncor= a 0 43 54 60 5 108 7 4 101 105 83 86 81 24 44 c 0 14 10 5 101 1 2 106 1 4 5 12 5 19 23 g 0 14 14 16 2 2 103 1 3 2 2 4 5 19 19 t 0 42 35 32 5 2 1 2 8 2 23 11 22 51 27
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m5; m=3/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.922632; wwawCAGCAAAAAta ; cor=; Ncor= a 25 26 41 22 2 79 4 2 67 72 64 77 67 12 34 c 12 11 7 5 74 0 2 75 2 4 1 0 1 10 16 g 16 13 13 11 2 0 73 1 1 1 0 1 0 14 14 t 27 30 19 42 2 1 1 2 10 3 15 2 12 44 16
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m1; m=4/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.914191; awawCAGCAAAAAta ; cor=; Ncor= a 34 28 49 48 4 80 3 1 73 78 70 79 69 16 38 c 14 10 5 4 73 1 1 84 2 4 1 2 1 14 19 g 17 14 11 11 2 1 81 0 3 2 0 1 4 14 12 t 21 34 21 23 7 4 1 1 8 2 15 4 12 42 17
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m3_rc; m=5/5; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.774694; wwaACAGCAAwAat- ; cor=; Ncor= a 23 23 39 48 2 61 0 3 61 61 18 54 33 11 0 c 9 10 6 2 58 0 0 61 1 1 2 3 5 14 0 g 12 10 5 6 0 2 65 1 4 2 2 4 13 13 0 t 22 23 16 10 6 3 1 1 0 2 44 5 15 28 0

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=15; shift=0; ncol=15; wwawCAGCAAAAAta ; Alignment reference a 25 26 41 22 2 79 4 2 67 72 64 77 67 12 34 c 12 11 7 5 74 0 2 75 2 4 1 0 1 10 16 g 16 13 13 11 2 0 73 1 1 1 0 1 0 14 14 t 27 30 19 42 2 1 1 2 10 3 15 2 12 44 16
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; wwawCAGCAAAAAta ; cor=; Ncor= a 25 26 41 22 2 79 4 2 67 72 64 77 67 12 34 c 12 11 7 5 74 0 2 75 2 4 1 0 1 10 16 g 16 13 13 11 2 0 73 1 1 1 0 1 0 14 14 t 27 30 19 42 2 1 1 2 10 3 15 2 12 44 16
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m1; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.981691; awawCAGCAAAAAta ; cor=; Ncor= a 34 28 49 48 4 80 3 1 73 78 70 79 69 16 38 c 14 10 5 4 73 1 1 84 2 4 1 2 1 14 19 g 17 14 11 11 2 1 81 0 3 2 0 1 4 14 12 t 21 34 21 23 7 4 1 1 8 2 15 4 12 42 17
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m4; m=3/5; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.922632; -wwdCAGCAAAAAta ; cor=; Ncor= a 0 25 29 24 2 80 6 2 71 76 66 78 65 13 34 c 0 12 10 5 77 0 3 79 1 5 2 2 3 11 12 g 0 12 15 26 2 1 72 0 2 1 0 0 0 13 17 t 0 33 28 27 1 1 1 1 8 0 14 2 14 45 19
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m1; m=4/5; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.91279; -wwwCAGCAAAAAta ; cor=; Ncor= a 0 43 54 60 5 108 7 4 101 105 83 86 81 24 44 c 0 14 10 5 101 1 2 106 1 4 5 12 5 19 23 g 0 14 14 16 2 2 103 1 3 2 2 4 5 19 19 t 0 42 35 32 5 2 1 2 8 2 23 11 22 51 27
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m3_rc; m=5/5; ncol2=14; w=0; offset=0; strand=R; shift=0; score= 0.8345; wwaACAGCAAwAat- ; cor=; Ncor= a 23 23 39 48 2 61 0 3 61 61 18 54 33 11 0 c 9 10 6 2 58 0 0 61 1 1 2 3 5 14 0 g 12 10 5 6 0 2 65 1 4 2 2 4 13 13 0 t 22 23 16 10 6 3 1 1 0 2 44 5 15 28 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; awawCAGCAAAAAta ; Alignment reference a 34 28 49 48 4 80 3 1 73 78 70 79 69 16 38 c 14 10 5 4 73 1 1 84 2 4 1 2 1 14 19 g 17 14 11 11 2 1 81 0 3 2 0 1 4 14 12 t 21 34 21 23 7 4 1 1 8 2 15 4 12 42 17
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score= 1; awawCAGCAAAAAta ; cor=; Ncor= a 34 28 49 48 4 80 3 1 73 78 70 79 69 16 38 c 14 10 5 4 73 1 1 84 2 4 1 2 1 14 19 g 17 14 11 11 2 1 81 0 3 2 0 1 4 14 12 t 21 34 21 23 7 4 1 1 8 2 15 4 12 42 17
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=2/5; ncol2=15; w=0; offset=0; strand=D; shift=0; score=0.981691; wwawCAGCAAAAAta ; cor=; Ncor= a 25 26 41 22 2 79 4 2 67 72 64 77 67 12 34 c 12 11 7 5 74 0 2 75 2 4 1 0 1 10 16 g 16 13 13 11 2 0 73 1 1 1 0 1 0 14 14 t 27 30 19 42 2 1 1 2 10 3 15 2 12 44 16
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=3/5; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.925761; -wwwCAGCAAAAAta ; cor=; Ncor= a 0 43 54 60 5 108 7 4 101 105 83 86 81 24 44 c 0 14 10 5 101 1 2 106 1 4 5 12 5 19 23 g 0 14 14 16 2 2 103 1 3 2 2 4 5 19 19 t 0 42 35 32 5 2 1 2 8 2 23 11 22 51 27
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=4/5; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.914191; -wwdCAGCAAAAAta ; cor=; Ncor= a 0 25 29 24 2 80 6 2 71 76 66 78 65 13 34 c 0 12 10 5 77 0 3 79 1 5 2 2 3 11 12 g 0 12 15 26 2 1 72 0 2 1 0 0 0 13 17 t 0 33 28 27 1 1 1 1 8 0 14 2 14 45 19
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=5/5; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.864997; wwaACAGCAAwAat- ; cor=; Ncor= a 23 23 39 48 2 61 0 3 61 61 18 54 33 11 0 c 9 10 6 2 58 0 0 61 1 1 2 3 5 14 0 g 12 10 5 6 0 2 65 1 4 2 2 4 13 13 0 t 22 23 16 10 6 3 1 1 0 2 44 5 15 28 0

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=14; shift=1; ncol=15; -atTwTTGCTGTtww ; Alignment reference a 0 28 15 5 44 2 0 1 1 3 6 10 16 23 22 c 0 13 13 4 2 2 4 1 65 2 0 6 5 10 12 g 0 14 5 3 2 1 1 61 0 0 58 2 6 10 9 t 0 11 33 54 18 61 61 3 0 61 2 48 39 23 23
oligos_7nt_mkv2_m3_shift1 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -atTwTTGCTGTtww ; cor=; Ncor= a 0 28 15 5 44 2 0 1 1 3 6 10 16 23 22 c 0 13 13 4 2 2 4 1 65 2 0 6 5 10 12 g 0 14 5 3 2 1 1 61 0 0 58 2 6 10 9 t 0 11 33 54 18 61 61 3 0 61 2 48 39 23 23
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m1_rc; m=2/5; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.864997; taTTTTTGCTGwtwt ; cor=; Ncor= a 17 42 12 4 15 2 8 1 1 4 7 23 21 34 21 c 12 14 4 1 0 2 3 0 81 1 2 11 11 14 17 g 19 14 1 2 1 4 2 84 1 1 73 4 5 10 14 t 38 16 69 79 70 78 73 1 3 80 4 48 49 28 34
oligos_7nt_mkv2_m5_rc_shift0 (oligos_7nt_mkv2_m5_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m5_rc; m=3/5; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score= 0.8345; taTTTTTGCTGwtww ; cor=; Ncor= a 16 44 12 2 15 3 10 2 1 1 2 42 19 30 27 c 14 14 0 1 0 1 1 1 73 0 2 11 13 13 16 g 16 10 1 0 1 4 2 75 2 0 74 5 7 11 12 t 34 12 67 77 64 72 67 2 4 79 2 22 41 26 25
oligos_6nt_mkv2_m1_rc_shift0 (oligos_6nt_mkv2_m1_rc)				; oligos_7nt_mkv2_m3 versus oligos_6nt_mkv2_m1_rc; m=4/5; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.813052; taTTTTTGCTGwww- ; cor=; Ncor= a 27 51 22 11 23 2 8 2 1 2 5 32 35 42 0 c 19 19 5 4 2 2 3 1 103 2 2 16 14 14 0 g 23 19 5 12 5 4 1 106 2 1 101 5 10 14 0 t 44 24 81 86 83 105 101 4 7 108 5 60 54 43 0
oligos_7nt_mkv2_m4_rc_shift0 (oligos_7nt_mkv2_m4_rc)				; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m4_rc; m=5/5; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.774694; taTTTTTGCTGhww- ; cor=; Ncor= a 19 45 14 2 14 0 8 1 1 1 1 27 28 33 0 c 17 13 0 0 0 1 2 0 72 1 2 26 15 12 0 g 12 11 3 2 2 5 1 79 3 0 77 5 10 12 0 t 34 13 65 78 66 76 71 2 6 80 2 24 29 25 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---wmTGATAAww ; Alignment reference a 0 0 0 21 21 0 0 60 0 60 60 21 23 c 0 0 0 9 20 0 0 0 0 0 0 6 7 g 0 0 0 13 8 0 60 0 0 0 0 14 14 t 0 0 0 17 11 60 0 0 60 0 0 19 16
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score= 1; ---wmTGATAAww ; cor=; Ncor= a 0 0 0 21 21 0 0 60 0 60 60 21 23 c 0 0 0 9 20 0 0 0 0 0 0 6 7 g 0 0 0 13 8 0 60 0 0 0 0 14 14 t 0 0 0 17 11 60 0 0 60 0 0 19 16
oligos_7nt_mkv2_m2_shift2 (oligos_7nt_mkv2_m2)				; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=2; score=0.84242; --wrCTGATAAtw ; cor=; Ncor= a 0 0 22 29 2 0 4 61 2 68 58 17 26 c 0 0 14 12 66 1 1 2 4 0 6 14 4 g 0 0 8 18 3 1 67 4 4 3 4 15 17 t 0 0 28 13 1 70 0 5 62 1 4 26 25
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m3; m=3/3; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.453021; wwwAATGATrw-- ; cor=; Ncor= a 22 23 21 63 63 0 0 63 0 22 19 0 0 c 9 8 13 0 0 0 0 0 0 11 11 0 0 g 11 9 7 0 0 0 63 0 0 16 10 0 0 t 21 23 22 0 0 63 0 0 63 14 23 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -wwwCAGCAAAAAta ; Alignment reference a 0 43 54 60 5 108 7 4 101 105 83 86 81 24 44 c 0 14 10 5 101 1 2 106 1 4 5 12 5 19 23 g 0 14 14 16 2 2 103 1 3 2 2 4 5 19 19 t 0 42 35 32 5 2 1 2 8 2 23 11 22 51 27
oligos_6nt_mkv2_m1_shift1 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/5; ncol2=14; w=0; offset=0; strand=D; shift=1; score= 1; -wwwCAGCAAAAAta ; cor=; Ncor= a 0 43 54 60 5 108 7 4 101 105 83 86 81 24 44 c 0 14 10 5 101 1 2 106 1 4 5 12 5 19 23 g 0 14 14 16 2 2 103 1 3 2 2 4 5 19 19 t 0 42 35 32 5 2 1 2 8 2 23 11 22 51 27
oligos_7nt_mkv2_m4_shift1 (oligos_7nt_mkv2_m4)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m4; m=2/5; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.980762; -wwdCAGCAAAAAta ; cor=; Ncor= a 0 25 29 24 2 80 6 2 71 76 66 78 65 13 34 c 0 12 10 5 77 0 3 79 1 5 2 2 3 11 12 g 0 12 15 26 2 1 72 0 2 1 0 0 0 13 17 t 0 33 28 27 1 1 1 1 8 0 14 2 14 45 19
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=3/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.925761; awawCAGCAAAAAta ; cor=; Ncor= a 34 28 49 48 4 80 3 1 73 78 70 79 69 16 38 c 14 10 5 4 73 1 1 84 2 4 1 2 1 14 19 g 17 14 11 11 2 1 81 0 3 2 0 1 4 14 12 t 21 34 21 23 7 4 1 1 8 2 15 4 12 42 17
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m5; m=4/5; ncol2=15; w=-1; offset=-1; strand=D; shift=0; score=0.91279; wwawCAGCAAAAAta ; cor=; Ncor= a 25 26 41 22 2 79 4 2 67 72 64 77 67 12 34 c 12 11 7 5 74 0 2 75 2 4 1 0 1 10 16 g 16 13 13 11 2 0 73 1 1 1 0 1 0 14 14 t 27 30 19 42 2 1 1 2 10 3 15 2 12 44 16
oligos_7nt_mkv2_m3_rc_shift0 (oligos_7nt_mkv2_m3_rc)				; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m3_rc; m=5/5; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.813052; wwaACAGCAAwAat- ; cor=; Ncor= a 23 23 39 48 2 61 0 3 61 61 18 54 33 11 0 c 9 10 6 2 58 0 0 61 1 1 2 3 5 14 0 g 12 10 5 6 0 2 65 1 4 2 2 4 13 13 0 t 22 23 16 10 6 3 1 1 0 2 44 5 15 28 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; wwwAATGATrw ; Alignment reference a 22 23 21 63 63 0 0 63 0 22 19 c 9 8 13 0 0 0 0 0 0 11 11 g 11 9 7 0 0 0 63 0 0 16 10 t 21 23 22 0 0 63 0 0 63 14 23
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwwAATGATrw ; cor=; Ncor= a 22 23 21 63 63 0 0 63 0 22 19 c 9 8 13 0 0 0 0 0 0 11 11 g 11 9 7 0 0 0 63 0 0 16 10 t 21 23 22 0 0 63 0 0 63 14 23
oligos_6nt_mkv2_m5_shift1 (oligos_6nt_mkv2_m5)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m5; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.698748; -gwAATAATra ; cor=; Ncor= a 0 19 26 79 79 0 79 79 0 32 35 c 0 19 17 0 0 0 0 0 0 9 16 g 0 24 8 0 0 0 0 0 0 22 15 t 0 17 28 0 0 79 0 0 79 16 13
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2)				; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m2; m=3/3; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.453021; ---wmTGATAA ; cor=; Ncor= a 0 0 0 21 21 0 0 60 0 60 60 c 0 0 0 9 20 0 0 0 0 0 0 g 0 0 0 13 8 0 60 0 0 0 0 t 0 0 0 17 11 60 0 0 60 0 0