One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/02/27/peak-motifs.2025-02-27.145114_2025-02-27.145114_qxtruW/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/2025/02/27/peak-motifs.2025-02-27.145114_2025-02-27.145114_qxtruW/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: dyads_m1_shift3 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m1_shift3 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=19; shift=3; ncol=22; ---waatAAAAAGAAAAATaaw ; Alignment reference a 0 0 0 70 81 115 30 142 160 162 173 172 31 164 166 156 157 148 35 125 80 75 c 0 0 0 36 25 19 17 19 7 6 8 2 5 3 3 10 9 15 12 19 32 24 g 0 0 0 30 36 19 23 11 4 3 7 9 144 6 5 5 14 9 13 6 38 31 t 0 0 0 53 47 36 119 17 18 18 1 6 9 16 15 18 9 17 129 39 39 59

dyads_m1_shift3 (dyads_m1)
; dyads_m1 versus dyads_m1; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=3; score= 1; ---waatAAAAAGAAAAATaaw ; cor=; Ncor= a 0 0 0 70 81 115 30 142 160 162 173 172 31 164 166 156 157 148 35 125 80 75 c 0 0 0 36 25 19 17 19 7 6 8 2 5 3 3 10 9 15 12 19 32 24 g 0 0 0 30 36 19 23 11 4 3 7 9 144 6 5 5 14 9 13 6 38 31 t 0 0 0 53 47 36 119 17 18 18 1 6 9 16 15 18 9 17 129 39 39 59

dyads_m2_rc_shift4 (dyads_m2_rc)
; dyads_m1 versus dyads_m2_rc; m=2/4; ncol2=19; w=0; offset=1; strand=R; shift=4; score=0.74659; ----wwatAAAAGAAAAAgara ; cor=; Ncor= a 0 0 0 0 63 68 121 29 157 165 158 161 10 152 150 148 149 147 33 104 46 65 c 0 0 0 0 35 30 16 17 7 4 4 5 1 9 13 10 9 11 11 24 16 31 g 0 0 0 0 30 32 17 18 7 8 12 10 162 11 10 12 8 7 114 22 79 43 t 0 0 0 0 53 51 27 117 10 4 7 5 8 9 8 11 15 16 23 31 40 42

dyads_m4_shift0 (dyads_m4)
; dyads_m1 versus dyads_m4; m=3/4; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.652105; aatAaarArAAAGAAAAAGAaw ; cor=; Ncor= a 36 40 24 72 63 64 31 73 28 78 75 84 12 82 90 85 95 86 14 83 62 33 c 17 15 11 7 9 3 11 4 7 6 7 0 3 2 1 5 1 4 6 3 10 10 g 23 20 22 8 12 20 48 9 54 7 5 11 78 4 4 6 0 4 69 5 13 19 t 23 24 42 12 15 12 9 13 10 8 12 4 6 11 4 3 3 5 10 8 14 37

dyads_m3_shift4 (dyads_m3)
; dyads_m1 versus dyads_m3; m=4/4; ncol2=20; w=0; offset=1; strand=D; shift=4; score=0.620635; ----waatAgaAGAAAAAGAAt ; cor=; Ncor= a 0 0 0 0 63 77 90 33 132 36 112 134 25 134 154 133 141 151 16 132 138 40 c 0 0 0 0 35 18 22 21 10 5 19 8 13 9 4 5 6 8 5 12 9 17 g 0 0 0 0 23 30 39 10 7 98 19 11 114 11 5 12 9 3 140 4 5 32 t 0 0 0 0 44 40 14 101 16 26 15 12 13 11 2 15 9 3 4 17 13 76

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 5 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; aatAaarArAAAGAAAAAGAawaw ; Alignment reference a 36 40 24 72 63 64 31 73 28 78 75 84 12 82 90 85 95 86 14 83 62 33 39 38 c 17 15 11 7 9 3 11 4 7 6 7 0 3 2 1 5 1 4 6 3 10 10 22 8 g 23 20 22 8 12 20 48 9 54 7 5 11 78 4 4 6 0 4 69 5 13 19 14 17 t 23 24 42 12 15 12 9 13 10 8 12 4 6 11 4 3 3 5 10 8 14 37 24 36

dyads_m4_shift0 (dyads_m4)
; dyads_m4 versus dyads_m4; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; aatAaarArAAAGAAAAAGAawaw ; cor=; Ncor= a 36 40 24 72 63 64 31 73 28 78 75 84 12 82 90 85 95 86 14 83 62 33 39 38 c 17 15 11 7 9 3 11 4 7 6 7 0 3 2 1 5 1 4 6 3 10 10 22 8 g 23 20 22 8 12 20 48 9 54 7 5 11 78 4 4 6 0 4 69 5 13 19 14 17 t 23 24 42 12 15 12 9 13 10 8 12 4 6 11 4 3 3 5 10 8 14 37 24 36

dyads_m3_shift4 (dyads_m3)
; dyads_m4 versus dyads_m3; m=2/4; ncol2=20; w=0; offset=4; strand=D; shift=4; score=0.690057; ----waatAgaAGAAAAAGAAtad ; cor=; Ncor= a 0 0 0 0 63 77 90 33 132 36 112 134 25 134 154 133 141 151 16 132 138 40 65 54 c 0 0 0 0 35 18 22 21 10 5 19 8 13 9 4 5 6 8 5 12 9 17 34 20 g 0 0 0 0 23 30 39 10 7 98 19 11 114 11 5 12 9 3 140 4 5 32 31 46 t 0 0 0 0 44 40 14 101 16 26 15 12 13 11 2 15 9 3 4 17 13 76 35 45

dyads_m1_shift3 (dyads_m1)
; dyads_m4 versus dyads_m1; m=3/4; ncol2=19; w=0; offset=3; strand=D; shift=3; score=0.652105; ---waatAAAAAGAAAAATaaw-- ; cor=; Ncor= a 0 0 0 70 81 115 30 142 160 162 173 172 31 164 166 156 157 148 35 125 80 75 0 0 c 0 0 0 36 25 19 17 19 7 6 8 2 5 3 3 10 9 15 12 19 32 24 0 0 g 0 0 0 30 36 19 23 11 4 3 7 9 144 6 5 5 14 9 13 6 38 31 0 0 t 0 0 0 53 47 36 119 17 18 18 1 6 9 16 15 18 9 17 129 39 39 59 0 0

dyads_m2_rc_shift4 (dyads_m2_rc)
; dyads_m4 versus dyads_m2_rc; m=4/4; ncol2=19; w=0; offset=4; strand=R; shift=4; score=0.648153; ----wwatAAAAGAAAAAgaraw- ; cor=; Ncor= a 0 0 0 0 63 68 121 29 157 165 158 161 10 152 150 148 149 147 33 104 46 65 57 0 c 0 0 0 0 35 30 16 17 7 4 4 5 1 9 13 10 9 11 11 24 16 31 38 0 g 0 0 0 0 30 32 17 18 7 8 12 10 162 11 10 12 8 7 114 22 79 43 30 0 t 0 0 0 0 53 51 27 117 10 4 7 5 8 9 8 11 15 16 23 31 40 42 56 0

One-to-n matrix alignment; reference matrix: dyads_m2_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift1 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=19; shift=1; ncol=20; -wtytcTTTTTCTTTTatww ; Alignment reference a 0 56 42 40 31 23 16 15 11 8 9 8 5 7 4 10 117 27 51 53 c 0 30 43 79 22 114 7 8 12 10 11 162 10 12 8 7 18 17 32 30 g 0 38 31 16 24 11 11 9 10 13 9 1 5 4 4 7 17 16 30 35 t 0 57 65 46 104 33 147 149 148 150 152 10 161 158 165 157 29 121 68 63

dyads_m2_shift1 (dyads_m2)
; dyads_m2 versus dyads_m2; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=1; score= 1; -wtytcTTTTTCTTTTatww ; cor=; Ncor= a 0 56 42 40 31 23 16 15 11 8 9 8 5 7 4 10 117 27 51 53 c 0 30 43 79 22 114 7 8 12 10 11 162 10 12 8 7 18 17 32 30 g 0 38 31 16 24 11 11 9 10 13 9 1 5 4 4 7 17 16 30 35 t 0 57 65 46 104 33 147 149 148 150 152 10 161 158 165 157 29 121 68 63

dyads_m3_rc_shift0 (dyads_m3_rc)
; dyads_m2 versus dyads_m3_rc; m=2/4; ncol2=20; w=-1; offset=-1; strand=R; shift=0; score=0.806724; htaTTCTTTTTCTtcTattw ; cor=; Ncor= a 45 35 76 13 17 4 3 9 15 2 11 13 12 15 26 16 101 14 40 44 c 46 31 32 5 4 140 3 9 12 5 11 114 11 19 98 7 10 39 30 23 g 20 34 17 9 12 5 8 6 5 4 9 13 8 19 5 10 21 22 18 35 t 54 65 40 138 132 16 151 141 133 154 134 25 134 112 36 132 33 90 77 63

dyads_m1_rc_shift2 (dyads_m1_rc)
; dyads_m2 versus dyads_m1_rc; m=3/4; ncol2=19; w=0; offset=1; strand=R; shift=2; score=0.74659; --wttATTTTTCTTTTTatt ; cor=; Ncor= a 0 0 59 39 39 129 17 9 18 15 16 9 6 1 18 18 17 119 36 47 c 0 0 31 38 6 13 9 14 5 5 6 144 9 7 3 4 11 23 19 36 g 0 0 24 32 19 12 15 9 10 3 3 5 2 8 6 7 19 17 19 25 t 0 0 75 80 125 35 148 157 156 166 164 31 172 173 162 160 142 30 115 81

dyads_m4_rc_shift0 (dyads_m4_rc)
; dyads_m2 versus dyads_m4_rc; m=4/4; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.648153; wtwtTCTTTTTCTTTyTytt ; cor=; Ncor= a 36 24 37 14 8 10 5 3 3 4 11 6 4 12 8 10 13 9 12 15 c 17 14 19 13 5 69 4 0 6 4 4 78 11 5 7 54 9 48 20 12 g 8 22 10 10 3 6 4 1 5 1 2 3 0 7 6 7 4 11 3 9 t 38 39 33 62 83 14 86 95 85 90 82 12 84 75 78 28 73 31 64 63

One-to-n matrix alignment; reference matrix: dyads_m3_shift4 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift4 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=20; shift=4; ncol=24; ----waatAgaAGAAAAAGAAtad ; Alignment reference a 0 0 0 0 63 77 90 33 132 36 112 134 25 134 154 133 141 151 16 132 138 40 65 54 c 0 0 0 0 35 18 22 21 10 5 19 8 13 9 4 5 6 8 5 12 9 17 34 20 g 0 0 0 0 23 30 39 10 7 98 19 11 114 11 5 12 9 3 140 4 5 32 31 46 t 0 0 0 0 44 40 14 101 16 26 15 12 13 11 2 15 9 3 4 17 13 76 35 45

dyads_m3_shift4 (dyads_m3)
; dyads_m3 versus dyads_m3; m=1/4; ncol2=20; w=0; offset=0; strand=D; shift=4; score= 1; ----waatAgaAGAAAAAGAAtad ; cor=; Ncor= a 0 0 0 0 63 77 90 33 132 36 112 134 25 134 154 133 141 151 16 132 138 40 65 54 c 0 0 0 0 35 18 22 21 10 5 19 8 13 9 4 5 6 8 5 12 9 17 34 20 g 0 0 0 0 23 30 39 10 7 98 19 11 114 11 5 12 9 3 140 4 5 32 31 46 t 0 0 0 0 44 40 14 101 16 26 15 12 13 11 2 15 9 3 4 17 13 76 35 45

dyads_m2_rc_shift4 (dyads_m2_rc)
; dyads_m3 versus dyads_m2_rc; m=2/4; ncol2=19; w=0; offset=0; strand=R; shift=4; score=0.806724; ----wwatAAAAGAAAAAgaraw- ; cor=; Ncor= a 0 0 0 0 63 68 121 29 157 165 158 161 10 152 150 148 149 147 33 104 46 65 57 0 c 0 0 0 0 35 30 16 17 7 4 4 5 1 9 13 10 9 11 11 24 16 31 38 0 g 0 0 0 0 30 32 17 18 7 8 12 10 162 11 10 12 8 7 114 22 79 43 30 0 t 0 0 0 0 53 51 27 117 10 4 7 5 8 9 8 11 15 16 23 31 40 42 56 0

dyads_m4_shift0 (dyads_m4)
; dyads_m3 versus dyads_m4; m=3/4; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.690057; aatAaarArAAAGAAAAAGAawaw ; cor=; Ncor= a 36 40 24 72 63 64 31 73 28 78 75 84 12 82 90 85 95 86 14 83 62 33 39 38 c 17 15 11 7 9 3 11 4 7 6 7 0 3 2 1 5 1 4 6 3 10 10 22 8 g 23 20 22 8 12 20 48 9 54 7 5 11 78 4 4 6 0 4 69 5 13 19 14 17 t 23 24 42 12 15 12 9 13 10 8 12 4 6 11 4 3 3 5 10 8 14 37 24 36

dyads_m1_shift3 (dyads_m1)
; dyads_m3 versus dyads_m1; m=4/4; ncol2=19; w=-1; offset=-1; strand=D; shift=3; score=0.620635; ---waatAAAAAGAAAAATaaw-- ; cor=; Ncor= a 0 0 0 70 81 115 30 142 160 162 173 172 31 164 166 156 157 148 35 125 80 75 0 0 c 0 0 0 36 25 19 17 19 7 6 8 2 5 3 3 10 9 15 12 19 32 24 0 0 g 0 0 0 30 36 19 23 11 4 3 7 9 144 6 5 5 14 9 13 6 38 31 0 0 t 0 0 0 53 47 36 119 17 18 18 1 6 9 16 15 18 9 17 129 39 39 59 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=10; shift=0; ncol=10; waCTCCAAwa ; Alignment reference a 69 84 0 8 14 0 242 242 66 91 c 41 58 256 0 243 256 0 13 52 61 g 48 56 1 1 0 1 2 2 52 50 t 99 59 0 248 0 0 13 0 87 55

dyads_m5_shift0 (dyads_m5)
; dyads_m5 versus dyads_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score= 1; waCTCCAAwa ; cor=; Ncor= a 69 84 0 8 14 0 242 242 66 91 c 41 58 256 0 243 256 0 13 52 61 g 48 56 1 1 0 1 2 2 52 50 t 99 59 0 248 0 0 13 0 87 55

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m1_shift3 (dyads_m1)				; dyads_m1; m=0 (reference); ncol1=19; shift=3; ncol=22; ---waatAAAAAGAAAAATaaw ; Alignment reference a 0 0 0 70 81 115 30 142 160 162 173 172 31 164 166 156 157 148 35 125 80 75 c 0 0 0 36 25 19 17 19 7 6 8 2 5 3 3 10 9 15 12 19 32 24 g 0 0 0 30 36 19 23 11 4 3 7 9 144 6 5 5 14 9 13 6 38 31 t 0 0 0 53 47 36 119 17 18 18 1 6 9 16 15 18 9 17 129 39 39 59
dyads_m1_shift3 (dyads_m1)				; dyads_m1 versus dyads_m1; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=3; score= 1; ---waatAAAAAGAAAAATaaw ; cor=; Ncor= a 0 0 0 70 81 115 30 142 160 162 173 172 31 164 166 156 157 148 35 125 80 75 c 0 0 0 36 25 19 17 19 7 6 8 2 5 3 3 10 9 15 12 19 32 24 g 0 0 0 30 36 19 23 11 4 3 7 9 144 6 5 5 14 9 13 6 38 31 t 0 0 0 53 47 36 119 17 18 18 1 6 9 16 15 18 9 17 129 39 39 59
dyads_m2_rc_shift4 (dyads_m2_rc)				; dyads_m1 versus dyads_m2_rc; m=2/4; ncol2=19; w=0; offset=1; strand=R; shift=4; score=0.74659; ----wwatAAAAGAAAAAgara ; cor=; Ncor= a 0 0 0 0 63 68 121 29 157 165 158 161 10 152 150 148 149 147 33 104 46 65 c 0 0 0 0 35 30 16 17 7 4 4 5 1 9 13 10 9 11 11 24 16 31 g 0 0 0 0 30 32 17 18 7 8 12 10 162 11 10 12 8 7 114 22 79 43 t 0 0 0 0 53 51 27 117 10 4 7 5 8 9 8 11 15 16 23 31 40 42
dyads_m4_shift0 (dyads_m4)				; dyads_m1 versus dyads_m4; m=3/4; ncol2=24; w=-3; offset=-3; strand=D; shift=0; score=0.652105; aatAaarArAAAGAAAAAGAaw ; cor=; Ncor= a 36 40 24 72 63 64 31 73 28 78 75 84 12 82 90 85 95 86 14 83 62 33 c 17 15 11 7 9 3 11 4 7 6 7 0 3 2 1 5 1 4 6 3 10 10 g 23 20 22 8 12 20 48 9 54 7 5 11 78 4 4 6 0 4 69 5 13 19 t 23 24 42 12 15 12 9 13 10 8 12 4 6 11 4 3 3 5 10 8 14 37
dyads_m3_shift4 (dyads_m3)				; dyads_m1 versus dyads_m3; m=4/4; ncol2=20; w=0; offset=1; strand=D; shift=4; score=0.620635; ----waatAgaAGAAAAAGAAt ; cor=; Ncor= a 0 0 0 0 63 77 90 33 132 36 112 134 25 134 154 133 141 151 16 132 138 40 c 0 0 0 0 35 18 22 21 10 5 19 8 13 9 4 5 6 8 5 12 9 17 g 0 0 0 0 23 30 39 10 7 98 19 11 114 11 5 12 9 3 140 4 5 32 t 0 0 0 0 44 40 14 101 16 26 15 12 13 11 2 15 9 3 4 17 13 76

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m4_shift0 (dyads_m4)				; dyads_m4; m=0 (reference); ncol1=24; shift=0; ncol=24; aatAaarArAAAGAAAAAGAawaw ; Alignment reference a 36 40 24 72 63 64 31 73 28 78 75 84 12 82 90 85 95 86 14 83 62 33 39 38 c 17 15 11 7 9 3 11 4 7 6 7 0 3 2 1 5 1 4 6 3 10 10 22 8 g 23 20 22 8 12 20 48 9 54 7 5 11 78 4 4 6 0 4 69 5 13 19 14 17 t 23 24 42 12 15 12 9 13 10 8 12 4 6 11 4 3 3 5 10 8 14 37 24 36
dyads_m4_shift0 (dyads_m4)				; dyads_m4 versus dyads_m4; m=1/4; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; aatAaarArAAAGAAAAAGAawaw ; cor=; Ncor= a 36 40 24 72 63 64 31 73 28 78 75 84 12 82 90 85 95 86 14 83 62 33 39 38 c 17 15 11 7 9 3 11 4 7 6 7 0 3 2 1 5 1 4 6 3 10 10 22 8 g 23 20 22 8 12 20 48 9 54 7 5 11 78 4 4 6 0 4 69 5 13 19 14 17 t 23 24 42 12 15 12 9 13 10 8 12 4 6 11 4 3 3 5 10 8 14 37 24 36
dyads_m3_shift4 (dyads_m3)				; dyads_m4 versus dyads_m3; m=2/4; ncol2=20; w=0; offset=4; strand=D; shift=4; score=0.690057; ----waatAgaAGAAAAAGAAtad ; cor=; Ncor= a 0 0 0 0 63 77 90 33 132 36 112 134 25 134 154 133 141 151 16 132 138 40 65 54 c 0 0 0 0 35 18 22 21 10 5 19 8 13 9 4 5 6 8 5 12 9 17 34 20 g 0 0 0 0 23 30 39 10 7 98 19 11 114 11 5 12 9 3 140 4 5 32 31 46 t 0 0 0 0 44 40 14 101 16 26 15 12 13 11 2 15 9 3 4 17 13 76 35 45
dyads_m1_shift3 (dyads_m1)				; dyads_m4 versus dyads_m1; m=3/4; ncol2=19; w=0; offset=3; strand=D; shift=3; score=0.652105; ---waatAAAAAGAAAAATaaw-- ; cor=; Ncor= a 0 0 0 70 81 115 30 142 160 162 173 172 31 164 166 156 157 148 35 125 80 75 0 0 c 0 0 0 36 25 19 17 19 7 6 8 2 5 3 3 10 9 15 12 19 32 24 0 0 g 0 0 0 30 36 19 23 11 4 3 7 9 144 6 5 5 14 9 13 6 38 31 0 0 t 0 0 0 53 47 36 119 17 18 18 1 6 9 16 15 18 9 17 129 39 39 59 0 0
dyads_m2_rc_shift4 (dyads_m2_rc)				; dyads_m4 versus dyads_m2_rc; m=4/4; ncol2=19; w=0; offset=4; strand=R; shift=4; score=0.648153; ----wwatAAAAGAAAAAgaraw- ; cor=; Ncor= a 0 0 0 0 63 68 121 29 157 165 158 161 10 152 150 148 149 147 33 104 46 65 57 0 c 0 0 0 0 35 30 16 17 7 4 4 5 1 9 13 10 9 11 11 24 16 31 38 0 g 0 0 0 0 30 32 17 18 7 8 12 10 162 11 10 12 8 7 114 22 79 43 30 0 t 0 0 0 0 53 51 27 117 10 4 7 5 8 9 8 11 15 16 23 31 40 42 56 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m2_shift1 (dyads_m2)				; dyads_m2; m=0 (reference); ncol1=19; shift=1; ncol=20; -wtytcTTTTTCTTTTatww ; Alignment reference a 0 56 42 40 31 23 16 15 11 8 9 8 5 7 4 10 117 27 51 53 c 0 30 43 79 22 114 7 8 12 10 11 162 10 12 8 7 18 17 32 30 g 0 38 31 16 24 11 11 9 10 13 9 1 5 4 4 7 17 16 30 35 t 0 57 65 46 104 33 147 149 148 150 152 10 161 158 165 157 29 121 68 63
dyads_m2_shift1 (dyads_m2)				; dyads_m2 versus dyads_m2; m=1/4; ncol2=19; w=0; offset=0; strand=D; shift=1; score= 1; -wtytcTTTTTCTTTTatww ; cor=; Ncor= a 0 56 42 40 31 23 16 15 11 8 9 8 5 7 4 10 117 27 51 53 c 0 30 43 79 22 114 7 8 12 10 11 162 10 12 8 7 18 17 32 30 g 0 38 31 16 24 11 11 9 10 13 9 1 5 4 4 7 17 16 30 35 t 0 57 65 46 104 33 147 149 148 150 152 10 161 158 165 157 29 121 68 63
dyads_m3_rc_shift0 (dyads_m3_rc)				; dyads_m2 versus dyads_m3_rc; m=2/4; ncol2=20; w=-1; offset=-1; strand=R; shift=0; score=0.806724; htaTTCTTTTTCTtcTattw ; cor=; Ncor= a 45 35 76 13 17 4 3 9 15 2 11 13 12 15 26 16 101 14 40 44 c 46 31 32 5 4 140 3 9 12 5 11 114 11 19 98 7 10 39 30 23 g 20 34 17 9 12 5 8 6 5 4 9 13 8 19 5 10 21 22 18 35 t 54 65 40 138 132 16 151 141 133 154 134 25 134 112 36 132 33 90 77 63
dyads_m1_rc_shift2 (dyads_m1_rc)				; dyads_m2 versus dyads_m1_rc; m=3/4; ncol2=19; w=0; offset=1; strand=R; shift=2; score=0.74659; --wttATTTTTCTTTTTatt ; cor=; Ncor= a 0 0 59 39 39 129 17 9 18 15 16 9 6 1 18 18 17 119 36 47 c 0 0 31 38 6 13 9 14 5 5 6 144 9 7 3 4 11 23 19 36 g 0 0 24 32 19 12 15 9 10 3 3 5 2 8 6 7 19 17 19 25 t 0 0 75 80 125 35 148 157 156 166 164 31 172 173 162 160 142 30 115 81
dyads_m4_rc_shift0 (dyads_m4_rc)				; dyads_m2 versus dyads_m4_rc; m=4/4; ncol2=24; w=-1; offset=-1; strand=R; shift=0; score=0.648153; wtwtTCTTTTTCTTTyTytt ; cor=; Ncor= a 36 24 37 14 8 10 5 3 3 4 11 6 4 12 8 10 13 9 12 15 c 17 14 19 13 5 69 4 0 6 4 4 78 11 5 7 54 9 48 20 12 g 8 22 10 10 3 6 4 1 5 1 2 3 0 7 6 7 4 11 3 9 t 38 39 33 62 83 14 86 95 85 90 82 12 84 75 78 28 73 31 64 63

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift4 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=20; shift=4; ncol=24; ----waatAgaAGAAAAAGAAtad ; Alignment reference a 0 0 0 0 63 77 90 33 132 36 112 134 25 134 154 133 141 151 16 132 138 40 65 54 c 0 0 0 0 35 18 22 21 10 5 19 8 13 9 4 5 6 8 5 12 9 17 34 20 g 0 0 0 0 23 30 39 10 7 98 19 11 114 11 5 12 9 3 140 4 5 32 31 46 t 0 0 0 0 44 40 14 101 16 26 15 12 13 11 2 15 9 3 4 17 13 76 35 45
dyads_m3_shift4 (dyads_m3)				; dyads_m3 versus dyads_m3; m=1/4; ncol2=20; w=0; offset=0; strand=D; shift=4; score= 1; ----waatAgaAGAAAAAGAAtad ; cor=; Ncor= a 0 0 0 0 63 77 90 33 132 36 112 134 25 134 154 133 141 151 16 132 138 40 65 54 c 0 0 0 0 35 18 22 21 10 5 19 8 13 9 4 5 6 8 5 12 9 17 34 20 g 0 0 0 0 23 30 39 10 7 98 19 11 114 11 5 12 9 3 140 4 5 32 31 46 t 0 0 0 0 44 40 14 101 16 26 15 12 13 11 2 15 9 3 4 17 13 76 35 45
dyads_m2_rc_shift4 (dyads_m2_rc)				; dyads_m3 versus dyads_m2_rc; m=2/4; ncol2=19; w=0; offset=0; strand=R; shift=4; score=0.806724; ----wwatAAAAGAAAAAgaraw- ; cor=; Ncor= a 0 0 0 0 63 68 121 29 157 165 158 161 10 152 150 148 149 147 33 104 46 65 57 0 c 0 0 0 0 35 30 16 17 7 4 4 5 1 9 13 10 9 11 11 24 16 31 38 0 g 0 0 0 0 30 32 17 18 7 8 12 10 162 11 10 12 8 7 114 22 79 43 30 0 t 0 0 0 0 53 51 27 117 10 4 7 5 8 9 8 11 15 16 23 31 40 42 56 0
dyads_m4_shift0 (dyads_m4)				; dyads_m3 versus dyads_m4; m=3/4; ncol2=24; w=-4; offset=-4; strand=D; shift=0; score=0.690057; aatAaarArAAAGAAAAAGAawaw ; cor=; Ncor= a 36 40 24 72 63 64 31 73 28 78 75 84 12 82 90 85 95 86 14 83 62 33 39 38 c 17 15 11 7 9 3 11 4 7 6 7 0 3 2 1 5 1 4 6 3 10 10 22 8 g 23 20 22 8 12 20 48 9 54 7 5 11 78 4 4 6 0 4 69 5 13 19 14 17 t 23 24 42 12 15 12 9 13 10 8 12 4 6 11 4 3 3 5 10 8 14 37 24 36
dyads_m1_shift3 (dyads_m1)				; dyads_m3 versus dyads_m1; m=4/4; ncol2=19; w=-1; offset=-1; strand=D; shift=3; score=0.620635; ---waatAAAAAGAAAAATaaw-- ; cor=; Ncor= a 0 0 0 70 81 115 30 142 160 162 173 172 31 164 166 156 157 148 35 125 80 75 0 0 c 0 0 0 36 25 19 17 19 7 6 8 2 5 3 3 10 9 15 12 19 32 24 0 0 g 0 0 0 30 36 19 23 11 4 3 7 9 144 6 5 5 14 9 13 6 38 31 0 0 t 0 0 0 53 47 36 119 17 18 18 1 6 9 16 15 18 9 17 129 39 39 59 0 0