One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.150529_2026-01-05.150529_HDOPDl/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/2026/01/05/peak-motifs.2026-01-05.150529_2026-01-05.150529_HDOPDl/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; arAAATCATtw ; Alignment reference a 81 86 229 237 223 15 21 211 17 52 66 c 51 40 7 6 14 8 206 19 12 60 53 g 62 70 11 5 9 13 12 6 18 62 61 t 58 56 5 4 6 216 13 16 205 78 72

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; arAAATCATtw ; cor=; Ncor= a 81 86 229 237 223 15 21 211 17 52 66 c 51 40 7 6 14 8 206 19 12 60 53 g 62 70 11 5 9 13 12 6 18 62 61 t 58 56 5 4 6 216 13 16 205 78 72

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift7 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift7 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=17; shift=7; ncol=24; -------wwtatATTTTAATgaww ; Alignment reference a 0 0 0 0 0 0 0 25 26 17 46 10 64 2 7 4 7 61 56 17 10 53 28 34 c 0 0 0 0 0 0 0 16 13 8 6 11 3 6 3 4 3 6 8 1 7 5 15 10 g 0 0 0 0 0 0 0 12 13 6 16 6 6 7 5 7 3 6 7 4 50 4 13 15 t 0 0 0 0 0 0 0 27 28 49 12 53 7 65 65 65 67 7 9 58 13 18 24 21

oligos_6nt_test_vs_ctrl_m4_shift7 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/2; ncol2=17; w=0; offset=0; strand=D; shift=7; score= 1; -------wwtatATTTTAATgaww ; cor=; Ncor= a 0 0 0 0 0 0 0 25 26 17 46 10 64 2 7 4 7 61 56 17 10 53 28 34 c 0 0 0 0 0 0 0 16 13 8 6 11 3 6 3 4 3 6 8 1 7 5 15 10 g 0 0 0 0 0 0 0 12 13 6 16 6 6 7 5 7 3 6 7 4 50 4 13 15 t 0 0 0 0 0 0 0 27 28 49 12 53 7 65 65 65 67 7 9 58 13 18 24 21

oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1_rc; m=2/2; ncol2=24; w=-7; offset=-7; strand=R; shift=0; score=0.534266; yywakTTTTTyTTTTTTwAtkavw ; cor=; Ncor= a 10 7 24 21 5 3 2 2 2 0 9 4 6 3 0 4 6 25 33 10 6 25 14 18 c 12 12 5 10 5 5 1 2 4 3 16 3 6 3 3 2 4 4 4 2 5 5 12 7 g 10 9 2 6 22 3 2 2 2 3 9 1 1 0 1 2 1 5 4 6 21 8 12 8 t 16 20 17 11 16 37 43 42 40 42 14 40 35 42 44 40 37 14 7 30 16 10 10 15

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=21; shift=3; ncol=24; ---ttTyTTTTTTyTTTwaTgavw ; Alignment reference a 0 0 0 13 12 9 11 4 3 5 3 9 3 6 3 4 7 42 55 13 18 49 24 28 c 0 0 0 16 20 5 33 4 6 1 4 4 8 49 6 2 6 12 11 4 8 12 25 16 g 0 0 0 18 11 6 14 2 4 5 9 3 2 4 2 3 5 10 6 11 49 9 23 20 t 0 0 0 45 49 72 34 82 79 81 76 76 79 33 81 83 74 28 20 64 17 22 20 28

oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/5; ncol2=21; w=0; offset=0; strand=D; shift=3; score= 1; ---ttTyTTTTTTyTTTwaTgavw ; cor=; Ncor= a 0 0 0 13 12 9 11 4 3 5 3 9 3 6 3 4 7 42 55 13 18 49 24 28 c 0 0 0 16 20 5 33 4 6 1 4 4 8 49 6 2 6 12 11 4 8 12 25 16 g 0 0 0 18 11 6 14 2 4 5 9 3 2 4 2 3 5 10 6 11 49 9 23 20 t 0 0 0 45 49 72 34 82 79 81 76 76 79 33 81 83 74 28 20 64 17 22 20 28

oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=2/5; ncol2=22; w=-1; offset=-1; strand=D; shift=2; score=0.778619; --tywTTyTTTTTTyTTaatgaww ; cor=; Ncor= a 0 0 7 6 28 6 3 4 3 0 3 4 1 2 7 6 1 31 30 11 8 27 14 19 c 0 0 5 12 3 5 3 16 4 1 3 1 3 2 20 2 4 6 4 2 5 7 9 5 g 0 0 7 8 3 0 6 8 1 7 7 2 1 0 6 2 3 1 4 7 25 7 9 7 t 0 0 28 21 13 36 35 19 39 39 34 40 42 43 14 37 39 9 9 27 9 6 15 16

oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/5; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.747514; yywakTTTTTyTTTTTTwAtkavw ; cor=; Ncor= a 10 7 24 21 5 3 2 2 2 0 9 4 6 3 0 4 6 25 33 10 6 25 14 18 c 12 12 5 10 5 5 1 2 4 3 16 3 6 3 3 2 4 4 4 2 5 5 12 7 g 10 9 2 6 22 3 2 2 2 3 9 1 1 0 1 2 1 5 4 6 21 8 12 8 t 16 20 17 11 16 37 43 42 40 42 14 40 35 42 44 40 37 14 7 30 16 10 10 15

oligos_7nt_test_vs_ctrl_m2_shift7 (oligos_7nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=4/5; ncol2=20; w=0; offset=4; strand=D; shift=7; score=0.503859; -------twwttTCTTTAAAGAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 8 12 21 9 7 2 4 3 1 2 33 34 32 7 34 27 25 c 0 0 0 0 0 0 0 6 5 3 2 3 2 28 5 3 3 2 2 0 1 2 3 4 g 0 0 0 0 0 0 0 8 9 4 4 3 2 1 0 2 2 3 3 5 28 2 3 2 t 0 0 0 0 0 0 0 18 14 12 25 27 34 7 32 34 33 2 1 3 4 2 7 9

oligos_7nt_test_vs_ctrl_m1_rc_shift7 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1_rc; m=5/5; ncol2=13; w=0; offset=4; strand=R; shift=7; score=0.458841; -------ttaTTTTTTTAww---- ; cor=; Ncor= a 0 0 0 0 0 0 0 99 108 262 42 31 33 25 31 24 37 343 148 127 0 0 0 0 c 0 0 0 0 0 0 0 73 83 47 32 19 20 25 26 15 25 30 83 73 0 0 0 0 g 0 0 0 0 0 0 0 95 106 48 19 22 17 15 15 26 21 25 77 87 0 0 0 0 t 0 0 0 0 0 0 0 174 144 84 348 369 371 376 369 376 358 43 133 154 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=13; shift=0; ncol=13; rdTcTTGAAATdy ; Alignment reference a 51 45 10 16 6 15 23 149 146 159 10 47 40 c 32 32 11 109 13 5 10 6 9 4 19 37 55 g 50 52 7 26 15 9 129 11 12 6 12 45 35 t 42 46 147 24 141 146 13 9 8 6 134 46 45

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; rdTcTTGAAATdy ; cor=; Ncor= a 51 45 10 16 6 15 23 149 146 159 10 47 40 c 32 32 11 109 13 5 10 6 9 4 19 37 55 g 50 52 7 26 15 9 129 11 12 6 12 45 35 t 42 46 147 24 141 146 13 9 8 6 134 46 45

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; twTAAATTTAwa ; Alignment reference a 48 70 13 157 134 169 12 31 17 168 55 66 c 44 25 6 8 21 5 9 10 13 9 45 37 g 38 45 9 13 10 9 5 21 8 6 25 44 t 65 55 167 17 30 12 169 133 157 12 70 48

oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; twTAAATTTAwa ; cor=; Ncor= a 48 70 13 157 134 169 12 31 17 168 55 66 c 44 25 6 8 21 5 9 10 13 9 45 37 g 38 45 9 13 10 9 5 21 8 6 25 44 t 65 55 167 17 30 12 169 133 157 12 70 48

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; awgAATcAATra ; Alignment reference a 44 36 15 101 104 4 18 99 93 2 28 34 c 22 16 14 3 3 5 73 4 4 3 17 27 g 21 27 62 1 3 4 11 1 5 2 39 23 t 24 32 20 6 1 98 9 7 9 104 27 27

oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; awgAATcAATra ; cor=; Ncor= a 44 36 15 101 104 4 18 99 93 2 28 34 c 22 16 14 3 3 5 73 4 4 3 17 27 g 21 27 62 1 3 4 11 1 5 2 39 23 t 24 32 20 6 1 98 9 7 9 104 27 27

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; twwttTCTTTAAAGAaawwa ; Alignment reference a 8 12 21 9 7 2 4 3 1 2 33 34 32 7 34 27 25 12 14 18 c 6 5 3 2 3 2 28 5 3 3 2 2 0 1 2 3 4 4 9 8 g 8 9 4 4 3 2 1 0 2 2 3 3 5 28 2 3 2 3 5 6 t 18 14 12 25 27 34 7 32 34 33 2 1 3 4 2 7 9 21 12 8

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; twwttTCTTTAAAGAaawwa ; cor=; Ncor= a 8 12 21 9 7 2 4 3 1 2 33 34 32 7 34 27 25 12 14 18 c 6 5 3 2 3 2 28 5 3 3 2 2 0 1 2 3 4 4 9 8 g 8 9 4 4 3 2 1 0 2 2 3 3 5 28 2 3 2 3 5 6 t 18 14 12 25 27 34 7 32 34 33 2 1 3 4 2 7 9 21 12 8

oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/3; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.506105; ttaTTTTTTTAww------- ; cor=; Ncor= a 99 108 262 42 31 33 25 31 24 37 343 148 127 0 0 0 0 0 0 0 c 73 83 47 32 19 20 25 26 15 25 30 83 73 0 0 0 0 0 0 0 g 95 106 48 19 22 17 15 15 26 21 25 77 87 0 0 0 0 0 0 0 t 174 144 84 348 369 371 376 369 376 358 43 133 154 0 0 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m3_rc_shift3 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/3; ncol2=21; w=0; offset=3; strand=R; shift=3; score=0.503859; ---wbtcAtwAAArAAAAAA ; cor=; Ncor= a 0 0 0 28 20 22 17 64 20 28 74 83 81 33 79 76 76 81 79 82 c 0 0 0 20 23 9 49 11 6 10 5 3 2 4 2 3 9 5 4 2 g 0 0 0 16 25 12 8 4 11 12 6 2 6 49 8 4 4 1 6 4 t 0 0 0 28 24 49 18 13 55 42 7 4 3 6 3 9 3 5 3 4

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift2 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=22; shift=2; ncol=24; --tywTTyTTTTTTyTTaatgaww ; Alignment reference a 0 0 7 6 28 6 3 4 3 0 3 4 1 2 7 6 1 31 30 11 8 27 14 19 c 0 0 5 12 3 5 3 16 4 1 3 1 3 2 20 2 4 6 4 2 5 7 9 5 g 0 0 7 8 3 0 6 8 1 7 7 2 1 0 6 2 3 1 4 7 25 7 9 7 t 0 0 28 21 13 36 35 19 39 39 34 40 42 43 14 37 39 9 9 27 9 6 15 16

oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/4; ncol2=22; w=0; offset=0; strand=D; shift=2; score= 1; --tywTTyTTTTTTyTTaatgaww ; cor=; Ncor= a 0 0 7 6 28 6 3 4 3 0 3 4 1 2 7 6 1 31 30 11 8 27 14 19 c 0 0 5 12 3 5 3 16 4 1 3 1 3 2 20 2 4 6 4 2 5 7 9 5 g 0 0 7 8 3 0 6 8 1 7 7 2 1 0 6 2 3 1 4 7 25 7 9 7 t 0 0 28 21 13 36 35 19 39 39 34 40 42 43 14 37 39 9 9 27 9 6 15 16

oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=2/4; ncol2=21; w=0; offset=1; strand=D; shift=3; score=0.778619; ---ttTyTTTTTTyTTTwaTgavw ; cor=; Ncor= a 0 0 0 13 12 9 11 4 3 5 3 9 3 6 3 4 7 42 55 13 18 49 24 28 c 0 0 0 16 20 5 33 4 6 1 4 4 8 49 6 2 6 12 11 4 8 12 25 16 g 0 0 0 18 11 6 14 2 4 5 9 3 2 4 2 3 5 10 6 11 49 9 23 20 t 0 0 0 45 49 72 34 82 79 81 76 76 79 33 81 83 74 28 20 64 17 22 20 28

oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/4; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.755585; yywakTTTTTyTTTTTTwAtkavw ; cor=; Ncor= a 10 7 24 21 5 3 2 2 2 0 9 4 6 3 0 4 6 25 33 10 6 25 14 18 c 12 12 5 10 5 5 1 2 4 3 16 3 6 3 3 2 4 4 4 2 5 5 12 7 g 10 9 2 6 22 3 2 2 2 3 9 1 1 0 1 2 1 5 4 6 21 8 12 8 t 16 20 17 11 16 37 43 42 40 42 14 40 35 42 44 40 37 14 7 30 16 10 10 15

oligos_7nt_test_vs_ctrl_m1_rc_shift7 (oligos_7nt_test_vs_ctrl_m1_rc)
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1_rc; m=4/4; ncol2=13; w=0; offset=5; strand=R; shift=7; score=0.457209; -------ttaTTTTTTTAww---- ; cor=; Ncor= a 0 0 0 0 0 0 0 99 108 262 42 31 33 25 31 24 37 343 148 127 0 0 0 0 c 0 0 0 0 0 0 0 73 83 47 32 19 20 25 26 15 25 30 83 73 0 0 0 0 g 0 0 0 0 0 0 0 95 106 48 19 22 17 15 15 26 21 25 77 87 0 0 0 0 t 0 0 0 0 0 0 0 174 144 84 348 369 371 376 369 376 358 43 133 154 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift7 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=13; shift=7; ncol=20; -------wwTAAAAAAAtaa ; Alignment reference a 0 0 0 0 0 0 0 154 133 43 358 376 369 376 371 369 348 84 144 174 c 0 0 0 0 0 0 0 87 77 25 21 26 15 15 17 22 19 48 106 95 g 0 0 0 0 0 0 0 73 83 30 25 15 26 25 20 19 32 47 83 73 t 0 0 0 0 0 0 0 127 148 343 37 24 31 25 33 31 42 262 108 99

oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=7; score= 1; -------wwTAAAAAAAtaa ; cor=; Ncor= a 0 0 0 0 0 0 0 154 133 43 358 376 369 376 371 369 348 84 144 174 c 0 0 0 0 0 0 0 87 77 25 21 26 15 15 17 22 19 48 106 95 g 0 0 0 0 0 0 0 73 83 30 25 15 26 25 20 19 32 47 83 73 t 0 0 0 0 0 0 0 127 148 343 37 24 31 25 33 31 42 262 108 99

oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=2/5; ncol2=20; w=-7; offset=-7; strand=D; shift=0; score=0.506105; twwttTCTTTAAAGAaawwa ; cor=; Ncor= a 8 12 21 9 7 2 4 3 1 2 33 34 32 7 34 27 25 12 14 18 c 6 5 3 2 3 2 28 5 3 3 2 2 0 1 2 3 4 4 9 8 g 8 9 4 4 3 2 1 0 2 2 3 3 5 28 2 3 2 3 5 6 t 18 14 12 25 27 34 7 32 34 33 2 1 3 4 2 7 9 21 12 8

oligos_6nt_test_vs_ctrl_m3_rc_shift3 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/5; ncol2=21; w=-4; offset=-4; strand=R; shift=3; score=0.458841; ---wbtcAtwAAArAAAAAA ; cor=; Ncor= a 0 0 0 28 20 22 17 64 20 28 74 83 81 33 79 76 76 81 79 82 c 0 0 0 20 23 9 49 11 6 10 5 3 2 4 2 3 9 5 4 2 g 0 0 0 16 25 12 8 4 11 12 6 2 6 49 8 4 4 1 6 4 t 0 0 0 28 24 49 18 13 55 42 7 4 3 6 3 9 3 5 3 4

oligos_6nt_test_vs_ctrl_m2_rc_shift3 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=4/5; ncol2=22; w=-4; offset=-4; strand=R; shift=3; score=0.457209; ---wwtcattAArAAAAAAr ; cor=; Ncor= a 0 0 0 16 15 6 9 27 9 9 39 37 14 43 42 40 34 39 39 19 c 0 0 0 7 9 7 25 7 4 1 3 2 6 0 1 2 7 7 1 8 g 0 0 0 5 9 7 5 2 4 6 4 2 20 2 3 1 3 1 4 16 t 0 0 0 19 14 27 8 11 30 31 1 6 7 2 1 4 3 0 3 4

oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=5/5; ncol2=24; w=-3; offset=-3; strand=D; shift=4; score=0.432044; ----wbtmaTwAAAAAArAA ; cor=; Ncor= a 0 0 0 0 15 10 10 16 30 7 14 37 40 44 42 35 40 14 42 40 c 0 0 0 0 8 12 8 21 6 4 5 1 2 1 0 1 1 9 3 2 g 0 0 0 0 7 12 5 5 2 4 4 4 2 3 3 6 3 16 3 4 t 0 0 0 0 18 14 25 6 10 33 25 6 4 0 3 6 4 9 0 2

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; wbtmaTwAAAAAArAAAAAmtwrr ; Alignment reference a 15 10 10 16 30 7 14 37 40 44 42 35 40 14 42 40 42 43 37 16 11 17 20 16 c 8 12 8 21 6 4 5 1 2 1 0 1 1 9 3 2 2 2 3 22 6 2 9 10 g 7 12 5 5 2 4 4 4 2 3 3 6 3 16 3 4 2 1 5 5 10 5 12 12 t 18 14 25 6 10 33 25 6 4 0 3 6 4 9 0 2 2 2 3 5 21 24 7 10

oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wbtmaTwAAAAAArAAAAAmtwrr ; cor=; Ncor= a 15 10 10 16 30 7 14 37 40 44 42 35 40 14 42 40 42 43 37 16 11 17 20 16 c 8 12 8 21 6 4 5 1 2 1 0 1 1 9 3 2 2 2 3 22 6 2 9 10 g 7 12 5 5 2 4 4 4 2 3 3 6 3 16 3 4 2 1 5 5 10 5 12 12 t 18 14 25 6 10 33 25 6 4 0 3 6 4 9 0 2 2 2 3 5 21 24 7 10

oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/5; ncol2=22; w=0; offset=0; strand=R; shift=0; score=0.755585; wwtcattAArAAAAAArAAwra-- ; cor=; Ncor= a 16 15 6 9 27 9 9 39 37 14 43 42 40 34 39 39 19 35 36 13 21 28 0 0 c 7 9 7 25 7 4 1 3 2 6 0 1 2 7 7 1 8 6 0 3 8 7 0 0 g 5 9 7 5 2 4 6 4 2 20 2 3 1 3 1 4 16 3 5 3 12 5 0 0 t 19 14 27 8 11 30 31 1 6 7 2 1 4 3 0 3 4 3 6 28 6 7 0 0

oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/5; ncol2=21; w=0; offset=0; strand=R; shift=0; score=0.747514; wbtcAtwAAArAAAAAArAaa--- ; cor=; Ncor= a 28 20 22 17 64 20 28 74 83 81 33 79 76 76 81 79 82 34 72 49 45 0 0 0 c 20 23 9 49 11 6 10 5 3 2 4 2 3 9 5 4 2 14 6 11 18 0 0 0 g 16 25 12 8 4 11 12 6 2 6 49 8 4 4 1 6 4 33 5 20 16 0 0 0 t 28 24 49 18 13 55 42 7 4 3 6 3 9 3 5 3 4 11 9 12 13 0 0 0

oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4_rc; m=4/5; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.534266; wwtcATTAAAATataww------- ; cor=; Ncor= a 21 24 18 13 58 9 7 67 65 65 65 7 53 12 49 28 27 0 0 0 0 0 0 0 c 15 13 4 50 4 7 6 3 7 5 7 6 6 16 6 13 12 0 0 0 0 0 0 0 g 10 15 5 7 1 8 6 3 4 3 6 3 11 6 8 13 16 0 0 0 0 0 0 0 t 34 28 53 10 17 56 61 7 4 7 2 64 10 46 17 26 25 0 0 0 0 0 0 0

oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=5/5; ncol2=13; w=0; offset=3; strand=D; shift=3; score=0.432044; ---wwTAAAAAAAtaa-------- ; cor=; Ncor= a 0 0 0 154 133 43 358 376 369 376 371 369 348 84 144 174 0 0 0 0 0 0 0 0 c 0 0 0 87 77 25 21 26 15 15 17 22 19 48 106 95 0 0 0 0 0 0 0 0 g 0 0 0 73 83 30 25 15 26 25 20 19 32 47 83 73 0 0 0 0 0 0 0 0 t 0 0 0 127 148 343 37 24 31 25 33 31 42 262 108 99 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=21; shift=3; ncol=24; ---ttTyTTTTTTyTTTwaTgavw ; Alignment reference a 0 0 0 13 12 9 11 4 3 5 3 9 3 6 3 4 7 42 55 13 18 49 24 28 c 0 0 0 16 20 5 33 4 6 1 4 4 8 49 6 2 6 12 11 4 8 12 25 16 g 0 0 0 18 11 6 14 2 4 5 9 3 2 4 2 3 5 10 6 11 49 9 23 20 t 0 0 0 45 49 72 34 82 79 81 76 76 79 33 81 83 74 28 20 64 17 22 20 28
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/5; ncol2=21; w=0; offset=0; strand=D; shift=3; score= 1; ---ttTyTTTTTTyTTTwaTgavw ; cor=; Ncor= a 0 0 0 13 12 9 11 4 3 5 3 9 3 6 3 4 7 42 55 13 18 49 24 28 c 0 0 0 16 20 5 33 4 6 1 4 4 8 49 6 2 6 12 11 4 8 12 25 16 g 0 0 0 18 11 6 14 2 4 5 9 3 2 4 2 3 5 10 6 11 49 9 23 20 t 0 0 0 45 49 72 34 82 79 81 76 76 79 33 81 83 74 28 20 64 17 22 20 28
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2; m=2/5; ncol2=22; w=-1; offset=-1; strand=D; shift=2; score=0.778619; --tywTTyTTTTTTyTTaatgaww ; cor=; Ncor= a 0 0 7 6 28 6 3 4 3 0 3 4 1 2 7 6 1 31 30 11 8 27 14 19 c 0 0 5 12 3 5 3 16 4 1 3 1 3 2 20 2 4 6 4 2 5 7 9 5 g 0 0 7 8 3 0 6 8 1 7 7 2 1 0 6 2 3 1 4 7 25 7 9 7 t 0 0 28 21 13 36 35 19 39 39 34 40 42 43 14 37 39 9 9 27 9 6 15 16
oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/5; ncol2=24; w=-3; offset=-3; strand=R; shift=0; score=0.747514; yywakTTTTTyTTTTTTwAtkavw ; cor=; Ncor= a 10 7 24 21 5 3 2 2 2 0 9 4 6 3 0 4 6 25 33 10 6 25 14 18 c 12 12 5 10 5 5 1 2 4 3 16 3 6 3 3 2 4 4 4 2 5 5 12 7 g 10 9 2 6 22 3 2 2 2 3 9 1 1 0 1 2 1 5 4 6 21 8 12 8 t 16 20 17 11 16 37 43 42 40 42 14 40 35 42 44 40 37 14 7 30 16 10 10 15
oligos_7nt_test_vs_ctrl_m2_shift7 (oligos_7nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m2; m=4/5; ncol2=20; w=0; offset=4; strand=D; shift=7; score=0.503859; -------twwttTCTTTAAAGAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 8 12 21 9 7 2 4 3 1 2 33 34 32 7 34 27 25 c 0 0 0 0 0 0 0 6 5 3 2 3 2 28 5 3 3 2 2 0 1 2 3 4 g 0 0 0 0 0 0 0 8 9 4 4 3 2 1 0 2 2 3 3 5 28 2 3 2 t 0 0 0 0 0 0 0 18 14 12 25 27 34 7 32 34 33 2 1 3 4 2 7 9
oligos_7nt_test_vs_ctrl_m1_rc_shift7 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1_rc; m=5/5; ncol2=13; w=0; offset=4; strand=R; shift=7; score=0.458841; -------ttaTTTTTTTAww---- ; cor=; Ncor= a 0 0 0 0 0 0 0 99 108 262 42 31 33 25 31 24 37 343 148 127 0 0 0 0 c 0 0 0 0 0 0 0 73 83 47 32 19 20 25 26 15 25 30 83 73 0 0 0 0 g 0 0 0 0 0 0 0 95 106 48 19 22 17 15 15 26 21 25 77 87 0 0 0 0 t 0 0 0 0 0 0 0 174 144 84 348 369 371 376 369 376 358 43 133 154 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; twwttTCTTTAAAGAaawwa ; Alignment reference a 8 12 21 9 7 2 4 3 1 2 33 34 32 7 34 27 25 12 14 18 c 6 5 3 2 3 2 28 5 3 3 2 2 0 1 2 3 4 4 9 8 g 8 9 4 4 3 2 1 0 2 2 3 3 5 28 2 3 2 3 5 6 t 18 14 12 25 27 34 7 32 34 33 2 1 3 4 2 7 9 21 12 8
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/3; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; twwttTCTTTAAAGAaawwa ; cor=; Ncor= a 8 12 21 9 7 2 4 3 1 2 33 34 32 7 34 27 25 12 14 18 c 6 5 3 2 3 2 28 5 3 3 2 2 0 1 2 3 4 4 9 8 g 8 9 4 4 3 2 1 0 2 2 3 3 5 28 2 3 2 3 5 6 t 18 14 12 25 27 34 7 32 34 33 2 1 3 4 2 7 9 21 12 8
oligos_7nt_test_vs_ctrl_m1_rc_shift0 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1_rc; m=2/3; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.506105; ttaTTTTTTTAww------- ; cor=; Ncor= a 99 108 262 42 31 33 25 31 24 37 343 148 127 0 0 0 0 0 0 0 c 73 83 47 32 19 20 25 26 15 25 30 83 73 0 0 0 0 0 0 0 g 95 106 48 19 22 17 15 15 26 21 25 77 87 0 0 0 0 0 0 0 t 174 144 84 348 369 371 376 369 376 358 43 133 154 0 0 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m3_rc_shift3 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/3; ncol2=21; w=0; offset=3; strand=R; shift=3; score=0.503859; ---wbtcAtwAAArAAAAAA ; cor=; Ncor= a 0 0 0 28 20 22 17 64 20 28 74 83 81 33 79 76 76 81 79 82 c 0 0 0 20 23 9 49 11 6 10 5 3 2 4 2 3 9 5 4 2 g 0 0 0 16 25 12 8 4 11 12 6 2 6 49 8 4 4 1 6 4 t 0 0 0 28 24 49 18 13 55 42 7 4 3 6 3 9 3 5 3 4

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=22; shift=2; ncol=24; --tywTTyTTTTTTyTTaatgaww ; Alignment reference a 0 0 7 6 28 6 3 4 3 0 3 4 1 2 7 6 1 31 30 11 8 27 14 19 c 0 0 5 12 3 5 3 16 4 1 3 1 3 2 20 2 4 6 4 2 5 7 9 5 g 0 0 7 8 3 0 6 8 1 7 7 2 1 0 6 2 3 1 4 7 25 7 9 7 t 0 0 28 21 13 36 35 19 39 39 34 40 42 43 14 37 39 9 9 27 9 6 15 16
oligos_6nt_test_vs_ctrl_m2_shift2 (oligos_6nt_test_vs_ctrl_m2)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/4; ncol2=22; w=0; offset=0; strand=D; shift=2; score= 1; --tywTTyTTTTTTyTTaatgaww ; cor=; Ncor= a 0 0 7 6 28 6 3 4 3 0 3 4 1 2 7 6 1 31 30 11 8 27 14 19 c 0 0 5 12 3 5 3 16 4 1 3 1 3 2 20 2 4 6 4 2 5 7 9 5 g 0 0 7 8 3 0 6 8 1 7 7 2 1 0 6 2 3 1 4 7 25 7 9 7 t 0 0 28 21 13 36 35 19 39 39 34 40 42 43 14 37 39 9 9 27 9 6 15 16
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m3; m=2/4; ncol2=21; w=0; offset=1; strand=D; shift=3; score=0.778619; ---ttTyTTTTTTyTTTwaTgavw ; cor=; Ncor= a 0 0 0 13 12 9 11 4 3 5 3 9 3 6 3 4 7 42 55 13 18 49 24 28 c 0 0 0 16 20 5 33 4 6 1 4 4 8 49 6 2 6 12 11 4 8 12 25 16 g 0 0 0 18 11 6 14 2 4 5 9 3 2 4 2 3 5 10 6 11 49 9 23 20 t 0 0 0 45 49 72 34 82 79 81 76 76 79 33 81 83 74 28 20 64 17 22 20 28
oligos_6nt_test_vs_ctrl_m1_rc_shift0 (oligos_6nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1_rc; m=3/4; ncol2=24; w=-2; offset=-2; strand=R; shift=0; score=0.755585; yywakTTTTTyTTTTTTwAtkavw ; cor=; Ncor= a 10 7 24 21 5 3 2 2 2 0 9 4 6 3 0 4 6 25 33 10 6 25 14 18 c 12 12 5 10 5 5 1 2 4 3 16 3 6 3 3 2 4 4 4 2 5 5 12 7 g 10 9 2 6 22 3 2 2 2 3 9 1 1 0 1 2 1 5 4 6 21 8 12 8 t 16 20 17 11 16 37 43 42 40 42 14 40 35 42 44 40 37 14 7 30 16 10 10 15
oligos_7nt_test_vs_ctrl_m1_rc_shift7 (oligos_7nt_test_vs_ctrl_m1_rc)				; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1_rc; m=4/4; ncol2=13; w=0; offset=5; strand=R; shift=7; score=0.457209; -------ttaTTTTTTTAww---- ; cor=; Ncor= a 0 0 0 0 0 0 0 99 108 262 42 31 33 25 31 24 37 343 148 127 0 0 0 0 c 0 0 0 0 0 0 0 73 83 47 32 19 20 25 26 15 25 30 83 73 0 0 0 0 g 0 0 0 0 0 0 0 95 106 48 19 22 17 15 15 26 21 25 77 87 0 0 0 0 t 0 0 0 0 0 0 0 174 144 84 348 369 371 376 369 376 358 43 133 154 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=13; shift=7; ncol=20; -------wwTAAAAAAAtaa ; Alignment reference a 0 0 0 0 0 0 0 154 133 43 358 376 369 376 371 369 348 84 144 174 c 0 0 0 0 0 0 0 87 77 25 21 26 15 15 17 22 19 48 106 95 g 0 0 0 0 0 0 0 73 83 30 25 15 26 25 20 19 32 47 83 73 t 0 0 0 0 0 0 0 127 148 343 37 24 31 25 33 31 42 262 108 99
oligos_7nt_test_vs_ctrl_m1_shift7 (oligos_7nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=7; score= 1; -------wwTAAAAAAAtaa ; cor=; Ncor= a 0 0 0 0 0 0 0 154 133 43 358 376 369 376 371 369 348 84 144 174 c 0 0 0 0 0 0 0 87 77 25 21 26 15 15 17 22 19 48 106 95 g 0 0 0 0 0 0 0 73 83 30 25 15 26 25 20 19 32 47 83 73 t 0 0 0 0 0 0 0 127 148 343 37 24 31 25 33 31 42 262 108 99
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m2; m=2/5; ncol2=20; w=-7; offset=-7; strand=D; shift=0; score=0.506105; twwttTCTTTAAAGAaawwa ; cor=; Ncor= a 8 12 21 9 7 2 4 3 1 2 33 34 32 7 34 27 25 12 14 18 c 6 5 3 2 3 2 28 5 3 3 2 2 0 1 2 3 4 4 9 8 g 8 9 4 4 3 2 1 0 2 2 3 3 5 28 2 3 2 3 5 6 t 18 14 12 25 27 34 7 32 34 33 2 1 3 4 2 7 9 21 12 8
oligos_6nt_test_vs_ctrl_m3_rc_shift3 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/5; ncol2=21; w=-4; offset=-4; strand=R; shift=3; score=0.458841; ---wbtcAtwAAArAAAAAA ; cor=; Ncor= a 0 0 0 28 20 22 17 64 20 28 74 83 81 33 79 76 76 81 79 82 c 0 0 0 20 23 9 49 11 6 10 5 3 2 4 2 3 9 5 4 2 g 0 0 0 16 25 12 8 4 11 12 6 2 6 49 8 4 4 1 6 4 t 0 0 0 28 24 49 18 13 55 42 7 4 3 6 3 9 3 5 3 4
oligos_6nt_test_vs_ctrl_m2_rc_shift3 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=4/5; ncol2=22; w=-4; offset=-4; strand=R; shift=3; score=0.457209; ---wwtcattAArAAAAAAr ; cor=; Ncor= a 0 0 0 16 15 6 9 27 9 9 39 37 14 43 42 40 34 39 39 19 c 0 0 0 7 9 7 25 7 4 1 3 2 6 0 1 2 7 7 1 8 g 0 0 0 5 9 7 5 2 4 6 4 2 20 2 3 1 3 1 4 16 t 0 0 0 19 14 27 8 11 30 31 1 6 7 2 1 4 3 0 3 4
oligos_6nt_test_vs_ctrl_m1_shift4 (oligos_6nt_test_vs_ctrl_m1)				; oligos_7nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=5/5; ncol2=24; w=-3; offset=-3; strand=D; shift=4; score=0.432044; ----wbtmaTwAAAAAArAA ; cor=; Ncor= a 0 0 0 0 15 10 10 16 30 7 14 37 40 44 42 35 40 14 42 40 c 0 0 0 0 8 12 8 21 6 4 5 1 2 1 0 1 1 9 3 2 g 0 0 0 0 7 12 5 5 2 4 4 4 2 3 3 6 3 16 3 4 t 0 0 0 0 18 14 25 6 10 33 25 6 4 0 3 6 4 9 0 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; wbtmaTwAAAAAArAAAAAmtwrr ; Alignment reference a 15 10 10 16 30 7 14 37 40 44 42 35 40 14 42 40 42 43 37 16 11 17 20 16 c 8 12 8 21 6 4 5 1 2 1 0 1 1 9 3 2 2 2 3 22 6 2 9 10 g 7 12 5 5 2 4 4 4 2 3 3 6 3 16 3 4 2 1 5 5 10 5 12 12 t 18 14 25 6 10 33 25 6 4 0 3 6 4 9 0 2 2 2 3 5 21 24 7 10
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/5; ncol2=24; w=0; offset=0; strand=D; shift=0; score= 1; wbtmaTwAAAAAArAAAAAmtwrr ; cor=; Ncor= a 15 10 10 16 30 7 14 37 40 44 42 35 40 14 42 40 42 43 37 16 11 17 20 16 c 8 12 8 21 6 4 5 1 2 1 0 1 1 9 3 2 2 2 3 22 6 2 9 10 g 7 12 5 5 2 4 4 4 2 3 3 6 3 16 3 4 2 1 5 5 10 5 12 12 t 18 14 25 6 10 33 25 6 4 0 3 6 4 9 0 2 2 2 3 5 21 24 7 10
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/5; ncol2=22; w=0; offset=0; strand=R; shift=0; score=0.755585; wwtcattAArAAAAAArAAwra-- ; cor=; Ncor= a 16 15 6 9 27 9 9 39 37 14 43 42 40 34 39 39 19 35 36 13 21 28 0 0 c 7 9 7 25 7 4 1 3 2 6 0 1 2 7 7 1 8 6 0 3 8 7 0 0 g 5 9 7 5 2 4 6 4 2 20 2 3 1 3 1 4 16 3 5 3 12 5 0 0 t 19 14 27 8 11 30 31 1 6 7 2 1 4 3 0 3 4 3 6 28 6 7 0 0
oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3_rc; m=3/5; ncol2=21; w=0; offset=0; strand=R; shift=0; score=0.747514; wbtcAtwAAArAAAAAArAaa--- ; cor=; Ncor= a 28 20 22 17 64 20 28 74 83 81 33 79 76 76 81 79 82 34 72 49 45 0 0 0 c 20 23 9 49 11 6 10 5 3 2 4 2 3 9 5 4 2 14 6 11 18 0 0 0 g 16 25 12 8 4 11 12 6 2 6 49 8 4 4 1 6 4 33 5 20 16 0 0 0 t 28 24 49 18 13 55 42 7 4 3 6 3 9 3 5 3 4 11 9 12 13 0 0 0
oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4_rc; m=4/5; ncol2=17; w=0; offset=0; strand=R; shift=0; score=0.534266; wwtcATTAAAATataww------- ; cor=; Ncor= a 21 24 18 13 58 9 7 67 65 65 65 7 53 12 49 28 27 0 0 0 0 0 0 0 c 15 13 4 50 4 7 6 3 7 5 7 6 6 16 6 13 12 0 0 0 0 0 0 0 g 10 15 5 7 1 8 6 3 4 3 6 3 11 6 8 13 16 0 0 0 0 0 0 0 t 34 28 53 10 17 56 61 7 4 7 2 64 10 46 17 26 25 0 0 0 0 0 0 0
oligos_7nt_test_vs_ctrl_m1_shift3 (oligos_7nt_test_vs_ctrl_m1)				; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=5/5; ncol2=13; w=0; offset=3; strand=D; shift=3; score=0.432044; ---wwTAAAAAAAtaa-------- ; cor=; Ncor= a 0 0 0 154 133 43 358 376 369 376 371 369 348 84 144 174 0 0 0 0 0 0 0 0 c 0 0 0 87 77 25 21 26 15 15 17 22 19 48 106 95 0 0 0 0 0 0 0 0 g 0 0 0 73 83 30 25 15 26 25 20 19 32 47 83 73 0 0 0 0 0 0 0 0 t 0 0 0 127 148 343 37 24 31 25 33 31 42 262 108 99 0 0 0 0 0 0 0 0