One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 8 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=14; shift=0; ncol=17; byCCAGGTCACasw--- ; Alignment reference a 56 38 22 54 254 0 0 0 0 256 4 172 46 75 0 0 0 c 70 96 185 184 1 2 0 0 256 0 229 28 75 56 0 0 0 g 64 53 21 7 1 254 256 0 0 0 12 20 76 58 0 0 0 t 66 69 28 11 0 0 0 256 0 0 11 36 59 67 0 0 0

positions_7nt_m1_shift0 (positions_7nt_m1) 0.928 0.866 10.155 0.870 0.954 0.843 0.970 4 5 9 3 4 4 4 4.714 1
; positions_6nt_m1 versus positions_7nt_m1; m=1/7; ncol2=15; w=14; offset=0; strand=D; shift=0; score= 4.7143; byCCAGGTCACCtkg-- ; cor=0.928; Ncor=0.866; logoDP=10.155; NIcor=0.870; NsEucl=0.954; SSD=0.843; NSW=0.970; rcor=4; rNcor=5; rlogoDP=9; rNIcor=3; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=4.714; match_rank=1 a 63 54 14 13 282 3 3 6 6 273 5 32 53 54 67 0 0 c 79 94 235 262 2 5 5 5 275 4 254 210 68 66 72 0 0 g 74 64 18 6 4 279 281 10 6 10 15 17 57 80 109 0 0 t 75 79 24 10 3 4 2 270 4 4 17 32 113 91 43 0 0

positions_7nt_m2_shift0 (positions_7nt_m2) 0.857 0.800 9.743 0.793 0.935 1.681 0.940 19 16 11 11 16 18 18 15.571 14
; positions_6nt_m1 versus positions_7nt_m2; m=2/7; ncol2=15; w=14; offset=0; strand=D; shift=0; score=15.5714; byCAAGGTCACCttg-- ; cor=0.857; Ncor=0.800; logoDP=9.743; NIcor=0.793; NsEucl=0.935; SSD=1.681; NSW=0.940; rcor=19; rNcor=16; rlogoDP=11; rNIcor=11; rNsEucl=16; rSSD=18; rNSW=18; rank_mean=15.571; match_rank=14 a 55 60 17 301 305 8 6 3 5 322 9 56 83 76 63 0 0 c 87 122 293 18 4 3 1 6 307 2 299 241 78 76 64 0 0 g 101 56 9 7 17 314 327 5 19 6 13 19 45 81 147 0 0 t 93 98 17 10 10 11 2 322 5 6 15 20 130 103 62 0 0

positions_7nt_m5_shift0 (positions_7nt_m5) 0.800 0.800 9.506 0.818 0.923 2.321 0.917 28 15 13 9 27 29 27 21.143 22
; positions_6nt_m1 versus positions_7nt_m5; m=3/7; ncol2=14; w=14; offset=0; strand=D; shift=0; score=21.1429; kbCCAGGTCAAGgt--- ; cor=0.800; Ncor=0.800; logoDP=9.506; NIcor=0.818; NsEucl=0.923; SSD=2.321; NSW=0.917; rcor=28; rNcor=15; rlogoDP=13; rNIcor=9; rNsEucl=27; rSSD=29; rNSW=27; rank_mean=21.143; match_rank=22 a 61 53 20 32 253 4 5 4 1 251 198 17 61 63 0 0 0 c 51 75 212 228 5 3 0 5 252 11 18 11 54 65 0 0 0 g 74 67 15 1 3 254 254 5 7 1 33 229 89 50 0 0 0 t 80 71 19 5 5 5 7 252 6 3 17 9 62 88 0 0 0

positions_7nt_m3_shift0 (positions_7nt_m3) 0.808 0.754 10.086 0.768 0.924 2.255 0.919 26 21 10 12 26 27 26 21.143 23
; positions_6nt_m1 versus positions_7nt_m3; m=4/7; ncol2=15; w=14; offset=0; strand=D; shift=0; score=21.1429; smCCAGGTCATGcyg-- ; cor=0.808; Ncor=0.754; logoDP=10.086; NIcor=0.768; NsEucl=0.924; SSD=2.255; NSW=0.919; rcor=26; rNcor=21; rlogoDP=10; rNIcor=12; rNsEucl=26; rSSD=27; rNSW=26; rank_mean=21.143; match_rank=23 a 44 53 13 15 186 0 3 2 3 192 6 13 41 42 45 0 0 c 54 54 154 175 1 0 0 3 191 3 14 18 85 51 33 0 0 g 52 43 15 1 4 195 191 5 3 0 16 149 37 31 74 0 0 t 48 48 16 7 7 3 4 188 1 3 162 18 35 74 46 0 0

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc) 0.829 0.829 4.015 0.172 0.928 2.014 0.928 21 12 35 37 21 21 20 23.857 26
; positions_6nt_m1 versus positions_6nt_m2_rc; m=5/7; ncol2=14; w=14; offset=0; strand=R; shift=0; score=23.8571; gvCCAGGTCATGgt--- ; cor=0.829; Ncor=0.829; logoDP=4.015; NIcor=0.172; NsEucl=0.928; SSD=2.014; NSW=0.928; rcor=21; rNcor=12; rlogoDP=35; rNIcor=37; rNsEucl=21; rSSD=21; rNSW=20; rank_mean=23.857; match_rank=26 a 51 52 14 30 203 0 1 0 0 205 14 16 49 46 0 0 0 c 51 55 156 163 0 0 0 0 205 0 14 19 50 51 0 0 0 g 61 53 17 1 2 204 204 0 0 0 32 153 61 34 0 0 0 t 42 45 18 11 0 1 0 205 0 0 145 17 45 74 0 0 0

positions_7nt_m4_shift0 (positions_7nt_m4) 0.797 0.744 9.618 0.754 0.922 2.383 0.915 30 24 12 15 29 32 31 24.714 28
; positions_6nt_m1 versus positions_7nt_m4; m=6/7; ncol2=15; w=14; offset=0; strand=D; shift=0; score=24.7143; ssCCAGGTCAGGgcr-- ; cor=0.797; Ncor=0.744; logoDP=9.618; NIcor=0.754; NsEucl=0.922; SSD=2.383; NSW=0.915; rcor=30; rNcor=24; rlogoDP=12; rNIcor=15; rNsEucl=29; rSSD=32; rNSW=31; rank_mean=24.714; match_rank=28 a 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 0 0 c 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 0 0 g 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 0 0 t 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64 0 0

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc) 0.797 0.656 5.189 0.212 0.921 2.434 0.913 31 32 28 35 30 34 32 31.714 36
; positions_6nt_m1 versus positions_6nt_m4_rc; m=7/7; ncol2=17; w=14; offset=0; strand=R; shift=0; score=31.7143; rscCAGGTCAGGttras ; cor=0.797; Ncor=0.656; logoDP=5.189; NIcor=0.212; NsEucl=0.921; SSD=2.434; NSW=0.913; rcor=31; rNcor=32; rlogoDP=28; rNIcor=35; rNsEucl=30; rSSD=34; rNSW=32; rank_mean=31.714; match_rank=36 a 47 35 24 6 158 0 0 1 0 160 8 12 24 23 67 47 34 c 34 44 86 142 0 0 0 0 159 0 12 18 35 37 24 39 52 g 41 46 26 5 0 160 159 1 0 0 136 122 27 26 45 39 42 t 38 35 24 7 2 0 1 158 1 0 4 8 74 74 24 35 32

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)																	; positions_6nt_m1; m=0 (reference); ncol1=14; shift=0; ncol=17; byCCAGGTCACasw--- ; Alignment reference a 56 38 22 54 254 0 0 0 0 256 4 172 46 75 0 0 0 c 70 96 185 184 1 2 0 0 256 0 229 28 75 56 0 0 0 g 64 53 21 7 1 254 256 0 0 0 12 20 76 58 0 0 0 t 66 69 28 11 0 0 0 256 0 0 11 36 59 67 0 0 0
positions_7nt_m1_shift0 (positions_7nt_m1)	0.928	0.866	10.155	0.870	0.954	0.843	0.970	4	5	9	3	4	4	4	4.714	1	; positions_6nt_m1 versus positions_7nt_m1; m=1/7; ncol2=15; w=14; offset=0; strand=D; shift=0; score= 4.7143; byCCAGGTCACCtkg-- ; cor=0.928; Ncor=0.866; logoDP=10.155; NIcor=0.870; NsEucl=0.954; SSD=0.843; NSW=0.970; rcor=4; rNcor=5; rlogoDP=9; rNIcor=3; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=4.714; match_rank=1 a 63 54 14 13 282 3 3 6 6 273 5 32 53 54 67 0 0 c 79 94 235 262 2 5 5 5 275 4 254 210 68 66 72 0 0 g 74 64 18 6 4 279 281 10 6 10 15 17 57 80 109 0 0 t 75 79 24 10 3 4 2 270 4 4 17 32 113 91 43 0 0
positions_7nt_m2_shift0 (positions_7nt_m2)	0.857	0.800	9.743	0.793	0.935	1.681	0.940	19	16	11	11	16	18	18	15.571	14	; positions_6nt_m1 versus positions_7nt_m2; m=2/7; ncol2=15; w=14; offset=0; strand=D; shift=0; score=15.5714; byCAAGGTCACCttg-- ; cor=0.857; Ncor=0.800; logoDP=9.743; NIcor=0.793; NsEucl=0.935; SSD=1.681; NSW=0.940; rcor=19; rNcor=16; rlogoDP=11; rNIcor=11; rNsEucl=16; rSSD=18; rNSW=18; rank_mean=15.571; match_rank=14 a 55 60 17 301 305 8 6 3 5 322 9 56 83 76 63 0 0 c 87 122 293 18 4 3 1 6 307 2 299 241 78 76 64 0 0 g 101 56 9 7 17 314 327 5 19 6 13 19 45 81 147 0 0 t 93 98 17 10 10 11 2 322 5 6 15 20 130 103 62 0 0
positions_7nt_m5_shift0 (positions_7nt_m5)	0.800	0.800	9.506	0.818	0.923	2.321	0.917	28	15	13	9	27	29	27	21.143	22	; positions_6nt_m1 versus positions_7nt_m5; m=3/7; ncol2=14; w=14; offset=0; strand=D; shift=0; score=21.1429; kbCCAGGTCAAGgt--- ; cor=0.800; Ncor=0.800; logoDP=9.506; NIcor=0.818; NsEucl=0.923; SSD=2.321; NSW=0.917; rcor=28; rNcor=15; rlogoDP=13; rNIcor=9; rNsEucl=27; rSSD=29; rNSW=27; rank_mean=21.143; match_rank=22 a 61 53 20 32 253 4 5 4 1 251 198 17 61 63 0 0 0 c 51 75 212 228 5 3 0 5 252 11 18 11 54 65 0 0 0 g 74 67 15 1 3 254 254 5 7 1 33 229 89 50 0 0 0 t 80 71 19 5 5 5 7 252 6 3 17 9 62 88 0 0 0
positions_7nt_m3_shift0 (positions_7nt_m3)	0.808	0.754	10.086	0.768	0.924	2.255	0.919	26	21	10	12	26	27	26	21.143	23	; positions_6nt_m1 versus positions_7nt_m3; m=4/7; ncol2=15; w=14; offset=0; strand=D; shift=0; score=21.1429; smCCAGGTCATGcyg-- ; cor=0.808; Ncor=0.754; logoDP=10.086; NIcor=0.768; NsEucl=0.924; SSD=2.255; NSW=0.919; rcor=26; rNcor=21; rlogoDP=10; rNIcor=12; rNsEucl=26; rSSD=27; rNSW=26; rank_mean=21.143; match_rank=23 a 44 53 13 15 186 0 3 2 3 192 6 13 41 42 45 0 0 c 54 54 154 175 1 0 0 3 191 3 14 18 85 51 33 0 0 g 52 43 15 1 4 195 191 5 3 0 16 149 37 31 74 0 0 t 48 48 16 7 7 3 4 188 1 3 162 18 35 74 46 0 0
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)	0.829	0.829	4.015	0.172	0.928	2.014	0.928	21	12	35	37	21	21	20	23.857	26	; positions_6nt_m1 versus positions_6nt_m2_rc; m=5/7; ncol2=14; w=14; offset=0; strand=R; shift=0; score=23.8571; gvCCAGGTCATGgt--- ; cor=0.829; Ncor=0.829; logoDP=4.015; NIcor=0.172; NsEucl=0.928; SSD=2.014; NSW=0.928; rcor=21; rNcor=12; rlogoDP=35; rNIcor=37; rNsEucl=21; rSSD=21; rNSW=20; rank_mean=23.857; match_rank=26 a 51 52 14 30 203 0 1 0 0 205 14 16 49 46 0 0 0 c 51 55 156 163 0 0 0 0 205 0 14 19 50 51 0 0 0 g 61 53 17 1 2 204 204 0 0 0 32 153 61 34 0 0 0 t 42 45 18 11 0 1 0 205 0 0 145 17 45 74 0 0 0
positions_7nt_m4_shift0 (positions_7nt_m4)	0.797	0.744	9.618	0.754	0.922	2.383	0.915	30	24	12	15	29	32	31	24.714	28	; positions_6nt_m1 versus positions_7nt_m4; m=6/7; ncol2=15; w=14; offset=0; strand=D; shift=0; score=24.7143; ssCCAGGTCAGGgcr-- ; cor=0.797; Ncor=0.744; logoDP=9.618; NIcor=0.754; NsEucl=0.922; SSD=2.383; NSW=0.915; rcor=30; rNcor=24; rlogoDP=12; rNIcor=15; rNsEucl=29; rSSD=32; rNSW=31; rank_mean=24.714; match_rank=28 a 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 0 0 c 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 0 0 g 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 0 0 t 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64 0 0
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)	0.797	0.656	5.189	0.212	0.921	2.434	0.913	31	32	28	35	30	34	32	31.714	36	; positions_6nt_m1 versus positions_6nt_m4_rc; m=7/7; ncol2=17; w=14; offset=0; strand=R; shift=0; score=31.7143; rscCAGGTCAGGttras ; cor=0.797; Ncor=0.656; logoDP=5.189; NIcor=0.212; NsEucl=0.921; SSD=2.434; NSW=0.913; rcor=31; rNcor=32; rlogoDP=28; rNIcor=35; rNsEucl=30; rSSD=34; rNSW=32; rank_mean=31.714; match_rank=36 a 47 35 24 6 158 0 0 1 0 160 8 12 24 23 67 47 34 c 34 44 86 142 0 0 0 0 159 0 12 18 35 37 24 39 52 g 41 46 26 5 0 160 159 1 0 0 136 122 27 26 45 39 42 t 38 35 24 7 2 0 1 158 1 0 4 8 74 74 24 35 32

One-to-n matrix alignment; reference matrix: dyads_m4_shift1 ; 5 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
dyads_m4_shift1 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=13; shift=1; ncol=15; -cyAAGGTCACCst- ; Alignment reference a 0 16 15 64 78 0 0 0 0 76 0 1 19 16 0 c 0 26 32 4 0 1 0 0 78 0 77 75 25 16 0 g 0 19 11 9 0 77 78 0 0 2 1 2 20 19 0 t 0 17 20 1 0 0 0 78 0 0 0 0 14 27 0

positions_7nt_m2_shift0 (positions_7nt_m2) 0.958 0.831 10.520 0.820 0.961 0.517 0.980 3 11 7 8 3 3 3 5.429 2
; dyads_m4 versus positions_7nt_m2; m=1/4; ncol2=15; w=13; offset=-1; strand=D; shift=0; score= 5.4286; byCAAGGTCACCttg ; cor=0.958; Ncor=0.831; logoDP=10.520; NIcor=0.820; NsEucl=0.961; SSD=0.517; NSW=0.980; rcor=3; rNcor=11; rlogoDP=7; rNIcor=8; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=5.429; match_rank=2 a 55 60 17 301 305 8 6 3 5 322 9 56 83 76 63 c 87 122 293 18 4 3 1 6 307 2 299 241 78 76 64 g 101 56 9 7 17 314 327 5 19 6 13 19 45 81 147 t 93 98 17 10 10 11 2 322 5 6 15 20 130 103 62

positions_7nt_m1_shift0 (positions_7nt_m1) 0.858 0.744 10.278 0.741 0.928 1.728 0.934 18 23 8 17 20 19 19 17.714 15
; dyads_m4 versus positions_7nt_m1; m=2/4; ncol2=15; w=13; offset=-1; strand=D; shift=0; score=17.7143; byCCAGGTCACCtkg ; cor=0.858; Ncor=0.744; logoDP=10.278; NIcor=0.741; NsEucl=0.928; SSD=1.728; NSW=0.934; rcor=18; rNcor=23; rlogoDP=8; rNIcor=17; rNsEucl=20; rSSD=19; rNSW=19; rank_mean=17.714; match_rank=15 a 63 54 14 13 282 3 3 6 6 273 5 32 53 54 67 c 79 94 235 262 2 5 5 5 275 4 254 210 68 66 72 g 74 64 18 6 4 279 281 10 6 10 15 17 57 80 109 t 75 79 24 10 3 4 2 270 4 4 17 32 113 91 43

positions_6nt_m1_shift0 (positions_6nt_m1) 0.822 0.763 12.308 0.763 0.920 2.189 0.916 23 20 1 14 31 24 28 20.143 20
; dyads_m4 versus positions_6nt_m1; m=3/4; ncol2=14; w=13; offset=-1; strand=D; shift=0; score=20.1429; byCCAGGTCACasw- ; cor=0.822; Ncor=0.763; logoDP=12.308; NIcor=0.763; NsEucl=0.920; SSD=2.189; NSW=0.916; rcor=23; rNcor=20; rlogoDP=1; rNIcor=14; rNsEucl=31; rSSD=24; rNSW=28; rank_mean=20.143; match_rank=20 a 56 38 22 54 254 0 0 0 0 256 4 172 46 75 0 c 70 96 185 184 1 2 0 0 256 0 229 28 75 56 0 g 64 53 21 7 1 254 256 0 0 0 12 20 76 58 0 t 66 69 28 11 0 0 0 256 0 0 11 36 59 67 0

oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4) 0.776 0.656 10.928 0.642 0.897 2.588 0.882 36 31 5 20 38 36 38 29.143 33
; dyads_m4 versus oligos_6nt_mkv4_m4; m=4/4; ncol2=11; w=11; offset=1; strand=D; shift=2; score=29.1429; --cvAGGTCAGsg-- ; cor=0.776; Ncor=0.656; logoDP=10.928; NIcor=0.642; NsEucl=0.897; SSD=2.588; NSW=0.882; rcor=36; rNcor=31; rlogoDP=5; rNIcor=20; rNsEucl=38; rSSD=36; rNSW=38; rank_mean=29.143; match_rank=33 a 0 0 226 281 963 0 0 0 0 961 15 236 236 0 0 c 0 0 281 294 9 10 0 1 977 3 93 253 211 0 0 g 0 0 231 275 4 967 977 1 0 12 821 340 327 0 0 t 0 0 239 127 1 0 0 975 0 1 48 148 203 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m4_shift1 (dyads_m4)																	; dyads_m4; m=0 (reference); ncol1=13; shift=1; ncol=15; -cyAAGGTCACCst- ; Alignment reference a 0 16 15 64 78 0 0 0 0 76 0 1 19 16 0 c 0 26 32 4 0 1 0 0 78 0 77 75 25 16 0 g 0 19 11 9 0 77 78 0 0 2 1 2 20 19 0 t 0 17 20 1 0 0 0 78 0 0 0 0 14 27 0
positions_7nt_m2_shift0 (positions_7nt_m2)	0.958	0.831	10.520	0.820	0.961	0.517	0.980	3	11	7	8	3	3	3	5.429	2	; dyads_m4 versus positions_7nt_m2; m=1/4; ncol2=15; w=13; offset=-1; strand=D; shift=0; score= 5.4286; byCAAGGTCACCttg ; cor=0.958; Ncor=0.831; logoDP=10.520; NIcor=0.820; NsEucl=0.961; SSD=0.517; NSW=0.980; rcor=3; rNcor=11; rlogoDP=7; rNIcor=8; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=5.429; match_rank=2 a 55 60 17 301 305 8 6 3 5 322 9 56 83 76 63 c 87 122 293 18 4 3 1 6 307 2 299 241 78 76 64 g 101 56 9 7 17 314 327 5 19 6 13 19 45 81 147 t 93 98 17 10 10 11 2 322 5 6 15 20 130 103 62
positions_7nt_m1_shift0 (positions_7nt_m1)	0.858	0.744	10.278	0.741	0.928	1.728	0.934	18	23	8	17	20	19	19	17.714	15	; dyads_m4 versus positions_7nt_m1; m=2/4; ncol2=15; w=13; offset=-1; strand=D; shift=0; score=17.7143; byCCAGGTCACCtkg ; cor=0.858; Ncor=0.744; logoDP=10.278; NIcor=0.741; NsEucl=0.928; SSD=1.728; NSW=0.934; rcor=18; rNcor=23; rlogoDP=8; rNIcor=17; rNsEucl=20; rSSD=19; rNSW=19; rank_mean=17.714; match_rank=15 a 63 54 14 13 282 3 3 6 6 273 5 32 53 54 67 c 79 94 235 262 2 5 5 5 275 4 254 210 68 66 72 g 74 64 18 6 4 279 281 10 6 10 15 17 57 80 109 t 75 79 24 10 3 4 2 270 4 4 17 32 113 91 43
positions_6nt_m1_shift0 (positions_6nt_m1)	0.822	0.763	12.308	0.763	0.920	2.189	0.916	23	20	1	14	31	24	28	20.143	20	; dyads_m4 versus positions_6nt_m1; m=3/4; ncol2=14; w=13; offset=-1; strand=D; shift=0; score=20.1429; byCCAGGTCACasw- ; cor=0.822; Ncor=0.763; logoDP=12.308; NIcor=0.763; NsEucl=0.920; SSD=2.189; NSW=0.916; rcor=23; rNcor=20; rlogoDP=1; rNIcor=14; rNsEucl=31; rSSD=24; rNSW=28; rank_mean=20.143; match_rank=20 a 56 38 22 54 254 0 0 0 0 256 4 172 46 75 0 c 70 96 185 184 1 2 0 0 256 0 229 28 75 56 0 g 64 53 21 7 1 254 256 0 0 0 12 20 76 58 0 t 66 69 28 11 0 0 0 256 0 0 11 36 59 67 0
oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4)	0.776	0.656	10.928	0.642	0.897	2.588	0.882	36	31	5	20	38	36	38	29.143	33	; dyads_m4 versus oligos_6nt_mkv4_m4; m=4/4; ncol2=11; w=11; offset=1; strand=D; shift=2; score=29.1429; --cvAGGTCAGsg-- ; cor=0.776; Ncor=0.656; logoDP=10.928; NIcor=0.642; NsEucl=0.897; SSD=2.588; NSW=0.882; rcor=36; rNcor=31; rlogoDP=5; rNIcor=20; rNsEucl=38; rSSD=36; rNSW=38; rank_mean=29.143; match_rank=33 a 0 0 226 281 963 0 0 0 0 961 15 236 236 0 0 c 0 0 281 294 9 10 0 1 977 3 93 253 211 0 0 g 0 0 231 275 4 967 977 1 0 12 821 340 327 0 0 t 0 0 239 127 1 0 0 975 0 1 48 148 203 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift3 ; 6 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_m2_shift3 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=14; shift=3; ncol=17; ---acCATGACCTGGbc ; Alignment reference a 0 0 0 74 45 17 145 0 0 205 0 1 0 11 18 45 42 c 0 0 0 34 61 153 32 0 0 0 204 204 2 1 17 53 61 g 0 0 0 51 50 19 14 0 205 0 0 0 0 163 156 55 51 t 0 0 0 46 49 16 14 205 0 0 1 0 203 30 14 52 51

positions_7nt_m3_rc_shift2 (positions_7nt_m3_rc) 0.991 0.925 4.998 0.415 0.984 0.102 0.996 1 1 29 28 1 1 1 8.857 3
; positions_6nt_m2 versus positions_7nt_m3_rc; m=1/5; ncol2=15; w=14; offset=-1; strand=R; shift=2; score= 8.8571; --crgCATGACCTGGks ; cor=0.991; Ncor=0.925; logoDP=4.998; NIcor=0.415; NsEucl=0.984; SSD=0.102; NSW=0.996; rcor=1; rNcor=1; rlogoDP=29; rNIcor=28; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=8.857; match_rank=3 a 0 0 46 74 35 18 162 3 1 188 4 3 7 7 16 48 48 c 0 0 74 31 37 149 16 0 3 5 191 195 4 1 15 43 52 g 0 0 33 51 85 18 14 3 191 3 0 0 1 175 154 54 54 t 0 0 45 42 41 13 6 192 3 2 3 0 186 15 13 53 44

positions_6nt_m4_shift0 (positions_6nt_m4) 0.904 0.744 11.750 0.749 0.946 1.147 0.959 7 22 3 16 7 10 8 10.429 5
; positions_6nt_m2 versus positions_6nt_m4; m=2/5; ncol2=17; w=14; offset=-3; strand=D; shift=0; score=10.4286; styaaCCTGACCTGgsy ; cor=0.904; Ncor=0.744; logoDP=11.750; NIcor=0.749; NsEucl=0.946; SSD=1.147; NSW=0.959; rcor=7; rNcor=22; rlogoDP=3; rNIcor=16; rNsEucl=7; rSSD=10; rNSW=8; rank_mean=10.429; match_rank=5 a 32 35 24 74 74 8 4 0 1 158 1 0 2 7 24 35 38 c 42 39 45 26 27 122 136 0 0 1 159 160 0 5 26 46 41 g 52 39 24 37 35 18 12 0 159 0 0 0 0 142 86 44 34 t 34 47 67 23 24 12 8 160 0 1 0 0 158 6 24 35 47

positions_7nt_m5_rc_shift3 (positions_7nt_m5_rc) 0.918 0.918 3.784 0.233 0.951 0.942 0.966 6 2 38 34 5 6 5 13.714 11
; positions_6nt_m2 versus positions_7nt_m5_rc; m=3/5; ncol2=14; w=14; offset=0; strand=R; shift=3; score=13.7143; ---acCTTGACCTGGvm ; cor=0.918; Ncor=0.918; logoDP=3.784; NIcor=0.233; NsEucl=0.951; SSD=0.942; NSW=0.966; rcor=6; rNcor=2; rlogoDP=38; rNIcor=34; rNsEucl=5; rSSD=6; rNSW=5; rank_mean=13.714; match_rank=11 a 0 0 0 88 62 9 17 3 6 252 7 5 5 5 19 71 80 c 0 0 0 50 89 229 33 1 7 5 254 254 3 1 15 67 74 g 0 0 0 65 54 11 18 11 252 5 0 3 5 228 212 75 51 t 0 0 0 63 61 17 198 251 1 4 5 4 253 32 20 53 61

positions_7nt_m4_rc_shift2 (positions_7nt_m4_rc) 0.902 0.842 4.364 0.346 0.946 1.145 0.959 9 7 31 29 6 9 7 14.000 12
; positions_6nt_m2 versus positions_7nt_m4_rc; m=4/5; ncol2=15; w=14; offset=-1; strand=R; shift=2; score= 14; --ygcCCTGACCTGGss ; cor=0.902; Ncor=0.842; logoDP=4.364; NIcor=0.346; NsEucl=0.946; SSD=1.145; NSW=0.959; rcor=9; rNcor=7; rlogoDP=31; rNIcor=29; rNsEucl=6; rSSD=9; rNSW=7; rank_mean=14.000; match_rank=12 a 0 0 64 83 45 20 17 3 3 302 1 2 6 1 23 73 84 c 0 0 117 79 192 242 297 7 5 24 327 332 13 7 39 92 102 g 0 0 74 111 56 44 15 4 331 8 7 3 2 316 245 109 85 t 0 0 85 67 47 34 11 326 1 6 5 3 319 16 33 66 69

positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc) 0.822 0.767 3.978 0.240 0.927 2.074 0.926 24 19 36 32 22 23 21 25.286 29
; positions_6nt_m2 versus positions_7nt_m1_rc; m=5/5; ncol2=15; w=14; offset=-1; strand=R; shift=2; score=25.2857; --cmaGGTGACCTGGrv ; cor=0.822; Ncor=0.767; logoDP=3.978; NIcor=0.240; NsEucl=0.927; SSD=2.074; NSW=0.926; rcor=24; rNcor=19; rlogoDP=36; rNIcor=32; rNsEucl=22; rSSD=23; rNSW=21; rank_mean=25.286; match_rank=29 a 0 0 43 91 113 32 17 4 4 270 2 4 3 10 24 79 75 c 0 0 109 80 57 17 15 10 6 10 281 279 4 6 18 64 74 g 0 0 72 66 68 210 254 4 275 5 5 5 2 262 235 94 79 t 0 0 67 54 53 32 5 273 6 6 3 3 282 13 14 54 63

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m2_shift3 (positions_6nt_m2)																	; positions_6nt_m2; m=0 (reference); ncol1=14; shift=3; ncol=17; ---acCATGACCTGGbc ; Alignment reference a 0 0 0 74 45 17 145 0 0 205 0 1 0 11 18 45 42 c 0 0 0 34 61 153 32 0 0 0 204 204 2 1 17 53 61 g 0 0 0 51 50 19 14 0 205 0 0 0 0 163 156 55 51 t 0 0 0 46 49 16 14 205 0 0 1 0 203 30 14 52 51
positions_7nt_m3_rc_shift2 (positions_7nt_m3_rc)	0.991	0.925	4.998	0.415	0.984	0.102	0.996	1	1	29	28	1	1	1	8.857	3	; positions_6nt_m2 versus positions_7nt_m3_rc; m=1/5; ncol2=15; w=14; offset=-1; strand=R; shift=2; score= 8.8571; --crgCATGACCTGGks ; cor=0.991; Ncor=0.925; logoDP=4.998; NIcor=0.415; NsEucl=0.984; SSD=0.102; NSW=0.996; rcor=1; rNcor=1; rlogoDP=29; rNIcor=28; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=8.857; match_rank=3 a 0 0 46 74 35 18 162 3 1 188 4 3 7 7 16 48 48 c 0 0 74 31 37 149 16 0 3 5 191 195 4 1 15 43 52 g 0 0 33 51 85 18 14 3 191 3 0 0 1 175 154 54 54 t 0 0 45 42 41 13 6 192 3 2 3 0 186 15 13 53 44
positions_6nt_m4_shift0 (positions_6nt_m4)	0.904	0.744	11.750	0.749	0.946	1.147	0.959	7	22	3	16	7	10	8	10.429	5	; positions_6nt_m2 versus positions_6nt_m4; m=2/5; ncol2=17; w=14; offset=-3; strand=D; shift=0; score=10.4286; styaaCCTGACCTGgsy ; cor=0.904; Ncor=0.744; logoDP=11.750; NIcor=0.749; NsEucl=0.946; SSD=1.147; NSW=0.959; rcor=7; rNcor=22; rlogoDP=3; rNIcor=16; rNsEucl=7; rSSD=10; rNSW=8; rank_mean=10.429; match_rank=5 a 32 35 24 74 74 8 4 0 1 158 1 0 2 7 24 35 38 c 42 39 45 26 27 122 136 0 0 1 159 160 0 5 26 46 41 g 52 39 24 37 35 18 12 0 159 0 0 0 0 142 86 44 34 t 34 47 67 23 24 12 8 160 0 1 0 0 158 6 24 35 47
positions_7nt_m5_rc_shift3 (positions_7nt_m5_rc)	0.918	0.918	3.784	0.233	0.951	0.942	0.966	6	2	38	34	5	6	5	13.714	11	; positions_6nt_m2 versus positions_7nt_m5_rc; m=3/5; ncol2=14; w=14; offset=0; strand=R; shift=3; score=13.7143; ---acCTTGACCTGGvm ; cor=0.918; Ncor=0.918; logoDP=3.784; NIcor=0.233; NsEucl=0.951; SSD=0.942; NSW=0.966; rcor=6; rNcor=2; rlogoDP=38; rNIcor=34; rNsEucl=5; rSSD=6; rNSW=5; rank_mean=13.714; match_rank=11 a 0 0 0 88 62 9 17 3 6 252 7 5 5 5 19 71 80 c 0 0 0 50 89 229 33 1 7 5 254 254 3 1 15 67 74 g 0 0 0 65 54 11 18 11 252 5 0 3 5 228 212 75 51 t 0 0 0 63 61 17 198 251 1 4 5 4 253 32 20 53 61
positions_7nt_m4_rc_shift2 (positions_7nt_m4_rc)	0.902	0.842	4.364	0.346	0.946	1.145	0.959	9	7	31	29	6	9	7	14.000	12	; positions_6nt_m2 versus positions_7nt_m4_rc; m=4/5; ncol2=15; w=14; offset=-1; strand=R; shift=2; score= 14; --ygcCCTGACCTGGss ; cor=0.902; Ncor=0.842; logoDP=4.364; NIcor=0.346; NsEucl=0.946; SSD=1.145; NSW=0.959; rcor=9; rNcor=7; rlogoDP=31; rNIcor=29; rNsEucl=6; rSSD=9; rNSW=7; rank_mean=14.000; match_rank=12 a 0 0 64 83 45 20 17 3 3 302 1 2 6 1 23 73 84 c 0 0 117 79 192 242 297 7 5 24 327 332 13 7 39 92 102 g 0 0 74 111 56 44 15 4 331 8 7 3 2 316 245 109 85 t 0 0 85 67 47 34 11 326 1 6 5 3 319 16 33 66 69
positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)	0.822	0.767	3.978	0.240	0.927	2.074	0.926	24	19	36	32	22	23	21	25.286	29	; positions_6nt_m2 versus positions_7nt_m1_rc; m=5/5; ncol2=15; w=14; offset=-1; strand=R; shift=2; score=25.2857; --cmaGGTGACCTGGrv ; cor=0.822; Ncor=0.767; logoDP=3.978; NIcor=0.240; NsEucl=0.927; SSD=2.074; NSW=0.926; rcor=24; rNcor=19; rlogoDP=36; rNIcor=32; rNsEucl=22; rSSD=23; rNSW=21; rank_mean=25.286; match_rank=29 a 0 0 43 91 113 32 17 4 4 270 2 4 3 10 24 79 75 c 0 0 109 80 57 17 15 10 6 10 281 279 4 6 18 64 74 g 0 0 72 66 68 210 254 4 275 5 5 5 2 262 235 94 79 t 0 0 67 54 53 32 5 273 6 6 3 3 282 13 14 54 63

One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m3_shift0 (positions_7nt_m3)
; positions_7nt_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; smCCAGGTCATGcyg ; Alignment reference a 44 53 13 15 186 0 3 2 3 192 6 13 41 42 45 c 54 54 154 175 1 0 0 3 191 3 14 18 85 51 33 g 52 43 15 1 4 195 191 5 3 0 16 149 37 31 74 t 48 48 16 7 7 3 4 188 1 3 162 18 35 74 46

positions_7nt_m5_shift0 (positions_7nt_m5) 0.895 0.836 8.758 0.852 0.945 1.204 0.957 10 9 20 4 8 11 9 10.143 4
; positions_7nt_m3 versus positions_7nt_m5; m=1/2; ncol2=14; w=14; offset=0; strand=D; shift=0; score=10.1429; kbCCAGGTCAAGgt- ; cor=0.895; Ncor=0.836; logoDP=8.758; NIcor=0.852; NsEucl=0.945; SSD=1.204; NSW=0.957; rcor=10; rNcor=9; rlogoDP=20; rNIcor=4; rNsEucl=8; rSSD=11; rNSW=9; rank_mean=10.143; match_rank=4 a 61 53 20 32 253 4 5 4 1 251 198 17 61 63 0 c 51 75 212 228 5 3 0 5 252 11 18 11 54 65 0 g 74 67 15 1 3 254 254 5 7 1 33 229 89 50 0 t 80 71 19 5 5 5 7 252 6 3 17 9 62 88 0

positions_7nt_m4_shift0 (positions_7nt_m4) 0.870 0.870 8.846 0.878 0.942 1.510 0.950 17 4 16 1 12 15 14 11.286 8
; positions_7nt_m3 versus positions_7nt_m4; m=2/2; ncol2=15; w=15; offset=0; strand=D; shift=0; score=11.2857; ssCCAGGTCAGGgcr ; cor=0.870; Ncor=0.870; logoDP=8.846; NIcor=0.878; NsEucl=0.942; SSD=1.510; NSW=0.950; rcor=17; rNcor=4; rlogoDP=16; rNIcor=1; rNsEucl=12; rSSD=15; rNSW=14; rank_mean=11.286; match_rank=8 a 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 c 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 g 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 t 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m3_shift0 (positions_7nt_m3)																	; positions_7nt_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; smCCAGGTCATGcyg ; Alignment reference a 44 53 13 15 186 0 3 2 3 192 6 13 41 42 45 c 54 54 154 175 1 0 0 3 191 3 14 18 85 51 33 g 52 43 15 1 4 195 191 5 3 0 16 149 37 31 74 t 48 48 16 7 7 3 4 188 1 3 162 18 35 74 46
positions_7nt_m5_shift0 (positions_7nt_m5)	0.895	0.836	8.758	0.852	0.945	1.204	0.957	10	9	20	4	8	11	9	10.143	4	; positions_7nt_m3 versus positions_7nt_m5; m=1/2; ncol2=14; w=14; offset=0; strand=D; shift=0; score=10.1429; kbCCAGGTCAAGgt- ; cor=0.895; Ncor=0.836; logoDP=8.758; NIcor=0.852; NsEucl=0.945; SSD=1.204; NSW=0.957; rcor=10; rNcor=9; rlogoDP=20; rNIcor=4; rNsEucl=8; rSSD=11; rNSW=9; rank_mean=10.143; match_rank=4 a 61 53 20 32 253 4 5 4 1 251 198 17 61 63 0 c 51 75 212 228 5 3 0 5 252 11 18 11 54 65 0 g 74 67 15 1 3 254 254 5 7 1 33 229 89 50 0 t 80 71 19 5 5 5 7 252 6 3 17 9 62 88 0
positions_7nt_m4_shift0 (positions_7nt_m4)	0.870	0.870	8.846	0.878	0.942	1.510	0.950	17	4	16	1	12	15	14	11.286	8	; positions_7nt_m3 versus positions_7nt_m4; m=2/2; ncol2=15; w=15; offset=0; strand=D; shift=0; score=11.2857; ssCCAGGTCAGGgcr ; cor=0.870; Ncor=0.870; logoDP=8.846; NIcor=0.878; NsEucl=0.942; SSD=1.510; NSW=0.950; rcor=17; rNcor=4; rlogoDP=16; rNIcor=1; rNsEucl=12; rSSD=15; rNSW=14; rank_mean=11.286; match_rank=8 a 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 c 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 g 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 t 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; bwGTAAATATTTACwv ; Alignment reference a 22 58 13 6 99 104 105 1 102 0 0 4 90 6 30 27 c 30 2 1 9 3 2 0 3 0 1 0 0 1 86 16 27 g 27 16 86 1 0 0 1 0 3 0 2 3 9 1 2 30 t 27 30 6 90 4 0 0 102 1 105 104 99 6 13 58 22

dyads_m2_shift1 (dyads_m2) 0.892 0.836 12.003 0.826 0.941 1.589 0.947 13 8 2 6 14 17 16 10.857 6
; dyads_m1 versus dyads_m2; m=1/1; ncol2=15; w=15; offset=1; strand=D; shift=1; score=10.8571; -wrCAAATATTTACwt ; cor=0.892; Ncor=0.836; logoDP=12.003; NIcor=0.826; NsEucl=0.941; SSD=1.589; NSW=0.947; rcor=13; rNcor=8; rlogoDP=2; rNIcor=6; rNsEucl=14; rSSD=17; rNSW=16; rank_mean=10.857; match_rank=6 a 0 135 121 19 289 293 299 0 299 3 1 5 274 23 88 77 c 0 38 35 257 10 6 2 6 0 2 1 2 2 230 64 76 g 0 54 88 7 0 3 3 4 9 4 2 11 18 10 20 69 t 0 82 65 26 10 7 5 299 1 300 305 291 15 46 137 87

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m1_shift0 (dyads_m1)																		; dyads_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; bwGTAAATATTTACwv ; Alignment reference a 22 58 13 6 99 104 105 1 102 0 0 4 90 6 30 27 c 30 2 1 9 3 2 0 3 0 1 0 0 1 86 16 27 g 27 16 86 1 0 0 1 0 3 0 2 3 9 1 2 30 t 27 30 6 90 4 0 0 102 1 105 104 99 6 13 58 22
dyads_m2_shift1 (dyads_m2)		0.892	0.836	12.003	0.826	0.941	1.589	0.947	13	8	2	6	14	17	16	10.857	6	; dyads_m1 versus dyads_m2; m=1/1; ncol2=15; w=15; offset=1; strand=D; shift=1; score=10.8571; -wrCAAATATTTACwt ; cor=0.892; Ncor=0.836; logoDP=12.003; NIcor=0.826; NsEucl=0.941; SSD=1.589; NSW=0.947; rcor=13; rNcor=8; rlogoDP=2; rNIcor=6; rNsEucl=14; rSSD=17; rNSW=16; rank_mean=10.857; match_rank=6 a 0 135 121 19 289 293 299 0 299 3 1 5 274 23 88 77 c 0 38 35 257 10 6 2 6 0 2 1 2 2 230 64 76 g 0 54 88 7 0 3 3 4 9 4 2 11 18 10 20 69 t 0 82 65 26 10 7 5 299 1 300 305 291 15 46 137 87

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 5 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=17; shift=0; ncol=17; styaaCCTGACCTGgsy ; Alignment reference a 32 35 24 74 74 8 4 0 1 158 1 0 2 7 24 35 38 c 42 39 45 26 27 122 136 0 0 1 159 160 0 5 26 46 41 g 52 39 24 37 35 18 12 0 159 0 0 0 0 142 86 44 34 t 34 47 67 23 24 12 8 160 0 1 0 0 158 6 24 35 47

positions_7nt_m4_rc_shift2 (positions_7nt_m4_rc) 0.961 0.848 4.057 0.241 0.968 0.465 0.984 2 6 33 31 2 2 2 11.143 7
; positions_6nt_m4 versus positions_7nt_m4_rc; m=1/4; ncol2=15; w=15; offset=2; strand=R; shift=2; score=11.1429; --ygcCCTGACCTGGss ; cor=0.961; Ncor=0.848; logoDP=4.057; NIcor=0.241; NsEucl=0.968; SSD=0.465; NSW=0.984; rcor=2; rNcor=6; rlogoDP=33; rNIcor=31; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=11.143; match_rank=7 a 0 0 64 83 45 20 17 3 3 302 1 2 6 1 23 73 84 c 0 0 117 79 192 242 297 7 5 24 327 332 13 7 39 92 102 g 0 0 74 111 56 44 15 4 331 8 7 3 2 316 245 109 85 t 0 0 85 67 47 34 11 326 1 6 5 3 319 16 33 66 69

positions_7nt_m3_rc_shift2 (positions_7nt_m3_rc) 0.872 0.770 4.727 0.321 0.942 1.524 0.949 15 18 30 30 13 16 15 19.571 18
; positions_6nt_m4 versus positions_7nt_m3_rc; m=2/4; ncol2=15; w=15; offset=2; strand=R; shift=2; score=19.5714; --crgCATGACCTGGks ; cor=0.872; Ncor=0.770; logoDP=4.727; NIcor=0.321; NsEucl=0.942; SSD=1.524; NSW=0.949; rcor=15; rNcor=18; rlogoDP=30; rNIcor=30; rNsEucl=13; rSSD=16; rNSW=15; rank_mean=19.571; match_rank=18 a 0 0 46 74 35 18 162 3 1 188 4 3 7 7 16 48 48 c 0 0 74 31 37 149 16 0 3 5 191 195 4 1 15 43 52 g 0 0 33 51 85 18 14 3 191 3 0 0 1 175 154 54 54 t 0 0 45 42 41 13 6 192 3 2 3 0 186 15 13 53 44

positions_7nt_m5_rc_shift3 (positions_7nt_m5_rc) 0.892 0.735 4.016 0.236 0.943 1.269 0.955 12 26 34 33 10 13 11 19.857 19
; positions_6nt_m4 versus positions_7nt_m5_rc; m=3/4; ncol2=14; w=14; offset=3; strand=R; shift=3; score=19.8571; ---acCTTGACCTGGvm ; cor=0.892; Ncor=0.735; logoDP=4.016; NIcor=0.236; NsEucl=0.943; SSD=1.269; NSW=0.955; rcor=12; rNcor=26; rlogoDP=34; rNIcor=33; rNsEucl=10; rSSD=13; rNSW=11; rank_mean=19.857; match_rank=19 a 0 0 0 88 62 9 17 3 6 252 7 5 5 5 19 71 80 c 0 0 0 50 89 229 33 1 7 5 254 254 3 1 15 67 74 g 0 0 0 65 54 11 18 11 252 5 0 3 5 228 212 75 51 t 0 0 0 63 61 17 198 251 1 4 5 4 253 32 20 53 61

positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc) 0.800 0.706 3.589 0.141 0.927 2.383 0.921 29 27 39 38 23 31 23 30.000 35
; positions_6nt_m4 versus positions_7nt_m1_rc; m=4/4; ncol2=15; w=15; offset=2; strand=R; shift=2; score= 30; --cmaGGTGACCTGGrv ; cor=0.800; Ncor=0.706; logoDP=3.589; NIcor=0.141; NsEucl=0.927; SSD=2.383; NSW=0.921; rcor=29; rNcor=27; rlogoDP=39; rNIcor=38; rNsEucl=23; rSSD=31; rNSW=23; rank_mean=30.000; match_rank=35 a 0 0 43 91 113 32 17 4 4 270 2 4 3 10 24 79 75 c 0 0 109 80 57 17 15 10 6 10 281 279 4 6 18 64 74 g 0 0 72 66 68 210 254 4 275 5 5 5 2 262 235 94 79 t 0 0 67 54 53 32 5 273 6 6 3 3 282 13 14 54 63

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)																	; positions_6nt_m4; m=0 (reference); ncol1=17; shift=0; ncol=17; styaaCCTGACCTGgsy ; Alignment reference a 32 35 24 74 74 8 4 0 1 158 1 0 2 7 24 35 38 c 42 39 45 26 27 122 136 0 0 1 159 160 0 5 26 46 41 g 52 39 24 37 35 18 12 0 159 0 0 0 0 142 86 44 34 t 34 47 67 23 24 12 8 160 0 1 0 0 158 6 24 35 47
positions_7nt_m4_rc_shift2 (positions_7nt_m4_rc)	0.961	0.848	4.057	0.241	0.968	0.465	0.984	2	6	33	31	2	2	2	11.143	7	; positions_6nt_m4 versus positions_7nt_m4_rc; m=1/4; ncol2=15; w=15; offset=2; strand=R; shift=2; score=11.1429; --ygcCCTGACCTGGss ; cor=0.961; Ncor=0.848; logoDP=4.057; NIcor=0.241; NsEucl=0.968; SSD=0.465; NSW=0.984; rcor=2; rNcor=6; rlogoDP=33; rNIcor=31; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=11.143; match_rank=7 a 0 0 64 83 45 20 17 3 3 302 1 2 6 1 23 73 84 c 0 0 117 79 192 242 297 7 5 24 327 332 13 7 39 92 102 g 0 0 74 111 56 44 15 4 331 8 7 3 2 316 245 109 85 t 0 0 85 67 47 34 11 326 1 6 5 3 319 16 33 66 69
positions_7nt_m3_rc_shift2 (positions_7nt_m3_rc)	0.872	0.770	4.727	0.321	0.942	1.524	0.949	15	18	30	30	13	16	15	19.571	18	; positions_6nt_m4 versus positions_7nt_m3_rc; m=2/4; ncol2=15; w=15; offset=2; strand=R; shift=2; score=19.5714; --crgCATGACCTGGks ; cor=0.872; Ncor=0.770; logoDP=4.727; NIcor=0.321; NsEucl=0.942; SSD=1.524; NSW=0.949; rcor=15; rNcor=18; rlogoDP=30; rNIcor=30; rNsEucl=13; rSSD=16; rNSW=15; rank_mean=19.571; match_rank=18 a 0 0 46 74 35 18 162 3 1 188 4 3 7 7 16 48 48 c 0 0 74 31 37 149 16 0 3 5 191 195 4 1 15 43 52 g 0 0 33 51 85 18 14 3 191 3 0 0 1 175 154 54 54 t 0 0 45 42 41 13 6 192 3 2 3 0 186 15 13 53 44
positions_7nt_m5_rc_shift3 (positions_7nt_m5_rc)	0.892	0.735	4.016	0.236	0.943	1.269	0.955	12	26	34	33	10	13	11	19.857	19	; positions_6nt_m4 versus positions_7nt_m5_rc; m=3/4; ncol2=14; w=14; offset=3; strand=R; shift=3; score=19.8571; ---acCTTGACCTGGvm ; cor=0.892; Ncor=0.735; logoDP=4.016; NIcor=0.236; NsEucl=0.943; SSD=1.269; NSW=0.955; rcor=12; rNcor=26; rlogoDP=34; rNIcor=33; rNsEucl=10; rSSD=13; rNSW=11; rank_mean=19.857; match_rank=19 a 0 0 0 88 62 9 17 3 6 252 7 5 5 5 19 71 80 c 0 0 0 50 89 229 33 1 7 5 254 254 3 1 15 67 74 g 0 0 0 65 54 11 18 11 252 5 0 3 5 228 212 75 51 t 0 0 0 63 61 17 198 251 1 4 5 4 253 32 20 53 61
positions_7nt_m1_rc_shift2 (positions_7nt_m1_rc)	0.800	0.706	3.589	0.141	0.927	2.383	0.921	29	27	39	38	23	31	23	30.000	35	; positions_6nt_m4 versus positions_7nt_m1_rc; m=4/4; ncol2=15; w=15; offset=2; strand=R; shift=2; score= 30; --cmaGGTGACCTGGrv ; cor=0.800; Ncor=0.706; logoDP=3.589; NIcor=0.141; NsEucl=0.927; SSD=2.383; NSW=0.921; rcor=29; rNcor=27; rlogoDP=39; rNIcor=38; rNsEucl=23; rSSD=31; rNSW=23; rank_mean=30.000; match_rank=35 a 0 0 43 91 113 32 17 4 4 270 2 4 3 10 24 79 75 c 0 0 109 80 57 17 15 10 6 10 281 279 4 6 18 64 74 g 0 0 72 66 68 210 254 4 275 5 5 5 2 262 235 94 79 t 0 0 67 54 53 32 5 273 6 6 3 3 282 13 14 54 63

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m4_shift0 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=15; shift=0; ncol=15; ssCCAGGTCAGGgcr ; Alignment reference a 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 c 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 g 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 t 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64

positions_7nt_m5_shift0 (positions_7nt_m5) 0.892 0.833 8.417 0.834 0.944 1.236 0.956 11 10 23 5 9 12 10 11.429 9
; positions_7nt_m4 versus positions_7nt_m5; m=1/1; ncol2=14; w=14; offset=0; strand=D; shift=0; score=11.4286; kbCCAGGTCAAGgt- ; cor=0.892; Ncor=0.833; logoDP=8.417; NIcor=0.834; NsEucl=0.944; SSD=1.236; NSW=0.956; rcor=11; rNcor=10; rlogoDP=23; rNIcor=5; rNsEucl=9; rSSD=12; rNSW=10; rank_mean=11.429; match_rank=9 a 61 53 20 32 253 4 5 4 1 251 198 17 61 63 0 c 51 75 212 228 5 3 0 5 252 11 18 11 54 65 0 g 74 67 15 1 3 254 254 5 7 1 33 229 89 50 0 t 80 71 19 5 5 5 7 252 6 3 17 9 62 88 0

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m4_shift0 (positions_7nt_m4)																		; positions_7nt_m4; m=0 (reference); ncol1=15; shift=0; ncol=15; ssCCAGGTCAGGgcr ; Alignment reference a 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 c 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 g 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 t 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64
positions_7nt_m5_shift0 (positions_7nt_m5)		0.892	0.833	8.417	0.834	0.944	1.236	0.956	11	10	23	5	9	12	10	11.429	9	; positions_7nt_m4 versus positions_7nt_m5; m=1/1; ncol2=14; w=14; offset=0; strand=D; shift=0; score=11.4286; kbCCAGGTCAAGgt- ; cor=0.892; Ncor=0.833; logoDP=8.417; NIcor=0.834; NsEucl=0.944; SSD=1.236; NSW=0.956; rcor=11; rNcor=10; rlogoDP=23; rNIcor=5; rNsEucl=9; rSSD=12; rNSW=10; rank_mean=11.429; match_rank=9 a 61 53 20 32 253 4 5 4 1 251 198 17 61 63 0 c 51 75 212 228 5 3 0 5 252 11 18 11 54 65 0 g 74 67 15 1 3 254 254 5 7 1 33 229 89 50 0 t 80 71 19 5 5 5 7 252 6 3 17 9 62 88 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 5 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; byCCAGGTCACCtkg ; Alignment reference a 63 54 14 13 282 3 3 6 6 273 5 32 53 54 67 c 79 94 235 262 2 5 5 5 275 4 254 210 68 66 72 g 74 64 18 6 4 279 281 10 6 10 15 17 57 80 109 t 75 79 24 10 3 4 2 270 4 4 17 32 113 91 43

positions_7nt_m2_shift0 (positions_7nt_m2) 0.872 0.872 8.103 0.873 0.942 1.498 0.950 16 3 26 2 11 14 13 12.143 10
; positions_7nt_m1 versus positions_7nt_m2; m=1/4; ncol2=15; w=15; offset=0; strand=D; shift=0; score=12.1429; byCAAGGTCACCttg ; cor=0.872; Ncor=0.872; logoDP=8.103; NIcor=0.873; NsEucl=0.942; SSD=1.498; NSW=0.950; rcor=16; rNcor=3; rlogoDP=26; rNIcor=2; rNsEucl=11; rSSD=14; rNSW=13; rank_mean=12.143; match_rank=10 a 55 60 17 301 305 8 6 3 5 322 9 56 83 76 63 c 87 122 293 18 4 3 1 6 307 2 299 241 78 76 64 g 101 56 9 7 17 314 327 5 19 6 13 19 45 81 147 t 93 98 17 10 10 11 2 322 5 6 15 20 130 103 62

positions_7nt_m3_shift0 (positions_7nt_m3) 0.807 0.807 8.613 0.826 0.929 2.240 0.925 27 14 21 7 19 26 22 19.429 17
; positions_7nt_m1 versus positions_7nt_m3; m=2/4; ncol2=15; w=15; offset=0; strand=D; shift=0; score=19.4286; smCCAGGTCATGcyg ; cor=0.807; Ncor=0.807; logoDP=8.613; NIcor=0.826; NsEucl=0.929; SSD=2.240; NSW=0.925; rcor=27; rNcor=14; rlogoDP=21; rNIcor=7; rNsEucl=19; rSSD=26; rNSW=22; rank_mean=19.429; match_rank=17 a 44 53 13 15 186 0 3 2 3 192 6 13 41 42 45 c 54 54 154 175 1 0 0 3 191 3 14 18 85 51 33 g 52 43 15 1 4 195 191 5 3 0 16 149 37 31 74 t 48 48 16 7 7 3 4 188 1 3 162 18 35 74 46

positions_7nt_m4_shift0 (positions_7nt_m4) 0.793 0.793 8.326 0.812 0.927 2.402 0.920 33 17 24 10 24 33 24 23.571 25
; positions_7nt_m1 versus positions_7nt_m4; m=3/4; ncol2=15; w=15; offset=0; strand=D; shift=0; score=23.5714; ssCCAGGTCAGGgcr ; cor=0.793; Ncor=0.793; logoDP=8.326; NIcor=0.812; NsEucl=0.927; SSD=2.402; NSW=0.920; rcor=33; rNcor=17; rlogoDP=24; rNIcor=10; rNsEucl=24; rSSD=33; rNSW=24; rank_mean=23.571; match_rank=25 a 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 c 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 g 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 t 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64

positions_7nt_m5_shift0 (positions_7nt_m5) 0.792 0.739 8.123 0.767 0.922 2.380 0.915 34 25 25 13 28 30 30 26.429 30
; positions_7nt_m1 versus positions_7nt_m5; m=4/4; ncol2=14; w=14; offset=0; strand=D; shift=0; score=26.4286; kbCCAGGTCAAGgt- ; cor=0.792; Ncor=0.739; logoDP=8.123; NIcor=0.767; NsEucl=0.922; SSD=2.380; NSW=0.915; rcor=34; rNcor=25; rlogoDP=25; rNIcor=13; rNsEucl=28; rSSD=30; rNSW=30; rank_mean=26.429; match_rank=30 a 61 53 20 32 253 4 5 4 1 251 198 17 61 63 0 c 51 75 212 228 5 3 0 5 252 11 18 11 54 65 0 g 74 67 15 1 3 254 254 5 7 1 33 229 89 50 0 t 80 71 19 5 5 5 7 252 6 3 17 9 62 88 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)																	; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; byCCAGGTCACCtkg ; Alignment reference a 63 54 14 13 282 3 3 6 6 273 5 32 53 54 67 c 79 94 235 262 2 5 5 5 275 4 254 210 68 66 72 g 74 64 18 6 4 279 281 10 6 10 15 17 57 80 109 t 75 79 24 10 3 4 2 270 4 4 17 32 113 91 43
positions_7nt_m2_shift0 (positions_7nt_m2)	0.872	0.872	8.103	0.873	0.942	1.498	0.950	16	3	26	2	11	14	13	12.143	10	; positions_7nt_m1 versus positions_7nt_m2; m=1/4; ncol2=15; w=15; offset=0; strand=D; shift=0; score=12.1429; byCAAGGTCACCttg ; cor=0.872; Ncor=0.872; logoDP=8.103; NIcor=0.873; NsEucl=0.942; SSD=1.498; NSW=0.950; rcor=16; rNcor=3; rlogoDP=26; rNIcor=2; rNsEucl=11; rSSD=14; rNSW=13; rank_mean=12.143; match_rank=10 a 55 60 17 301 305 8 6 3 5 322 9 56 83 76 63 c 87 122 293 18 4 3 1 6 307 2 299 241 78 76 64 g 101 56 9 7 17 314 327 5 19 6 13 19 45 81 147 t 93 98 17 10 10 11 2 322 5 6 15 20 130 103 62
positions_7nt_m3_shift0 (positions_7nt_m3)	0.807	0.807	8.613	0.826	0.929	2.240	0.925	27	14	21	7	19	26	22	19.429	17	; positions_7nt_m1 versus positions_7nt_m3; m=2/4; ncol2=15; w=15; offset=0; strand=D; shift=0; score=19.4286; smCCAGGTCATGcyg ; cor=0.807; Ncor=0.807; logoDP=8.613; NIcor=0.826; NsEucl=0.929; SSD=2.240; NSW=0.925; rcor=27; rNcor=14; rlogoDP=21; rNIcor=7; rNsEucl=19; rSSD=26; rNSW=22; rank_mean=19.429; match_rank=17 a 44 53 13 15 186 0 3 2 3 192 6 13 41 42 45 c 54 54 154 175 1 0 0 3 191 3 14 18 85 51 33 g 52 43 15 1 4 195 191 5 3 0 16 149 37 31 74 t 48 48 16 7 7 3 4 188 1 3 162 18 35 74 46
positions_7nt_m4_shift0 (positions_7nt_m4)	0.793	0.793	8.326	0.812	0.927	2.402	0.920	33	17	24	10	24	33	24	23.571	25	; positions_7nt_m1 versus positions_7nt_m4; m=3/4; ncol2=15; w=15; offset=0; strand=D; shift=0; score=23.5714; ssCCAGGTCAGGgcr ; cor=0.793; Ncor=0.793; logoDP=8.326; NIcor=0.812; NsEucl=0.927; SSD=2.402; NSW=0.920; rcor=33; rNcor=17; rlogoDP=24; rNIcor=10; rNsEucl=24; rSSD=33; rNSW=24; rank_mean=23.571; match_rank=25 a 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 c 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 g 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 t 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64
positions_7nt_m5_shift0 (positions_7nt_m5)	0.792	0.739	8.123	0.767	0.922	2.380	0.915	34	25	25	13	28	30	30	26.429	30	; positions_7nt_m1 versus positions_7nt_m5; m=4/4; ncol2=14; w=14; offset=0; strand=D; shift=0; score=26.4286; kbCCAGGTCAAGgt- ; cor=0.792; Ncor=0.739; logoDP=8.123; NIcor=0.767; NsEucl=0.922; SSD=2.380; NSW=0.915; rcor=34; rNcor=25; rlogoDP=25; rNIcor=13; rNsEucl=28; rSSD=30; rNSW=30; rank_mean=26.429; match_rank=30 a 61 53 20 32 253 4 5 4 1 251 198 17 61 63 0 c 51 75 212 228 5 3 0 5 252 11 18 11 54 65 0 g 74 67 15 1 3 254 254 5 7 1 33 229 89 50 0 t 80 71 19 5 5 5 7 252 6 3 17 9 62 88 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift2 ; 9 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=11; shift=2; ncol=17; --cvAGGTCAGsg---- ; Alignment reference a 0 0 226 281 963 0 0 0 0 961 15 236 236 0 0 0 0 c 0 0 281 294 9 10 0 1 977 3 93 253 211 0 0 0 0 g 0 0 231 275 4 967 977 1 0 12 821 340 327 0 0 0 0 t 0 0 239 127 1 0 0 975 0 1 48 148 203 0 0 0 0

positions_7nt_m4_shift0 (positions_7nt_m4) 0.903 0.662 9.289 0.648 0.934 1.068 0.951 8 29 15 19 17 7 12 15.286 13
; oligos_6nt_mkv4_m4 versus positions_7nt_m4; m=1/8; ncol2=15; w=11; offset=-2; strand=D; shift=0; score=15.2857; ssCCAGGTCAGGgcr-- ; cor=0.903; Ncor=0.662; logoDP=9.289; NIcor=0.648; NsEucl=0.934; SSD=1.068; NSW=0.951; rcor=8; rNcor=29; rlogoDP=15; rNIcor=19; rNsEucl=17; rSSD=7; rNSW=12; rank_mean=15.286; match_rank=13 a 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 0 0 c 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 0 0 g 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 0 0 t 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64 0 0

positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc) 0.922 0.597 3.908 0.102 0.939 0.896 0.959 5 36 37 39 15 5 6 20.429 21
; oligos_6nt_mkv4_m4 versus positions_6nt_m4_rc; m=2/8; ncol2=17; w=11; offset=-2; strand=R; shift=0; score=20.4286; rscCAGGTCAGGttras ; cor=0.922; Ncor=0.597; logoDP=3.908; NIcor=0.102; NsEucl=0.939; SSD=0.896; NSW=0.959; rcor=5; rNcor=36; rlogoDP=37; rNIcor=39; rNsEucl=15; rSSD=5; rNSW=6; rank_mean=20.429; match_rank=21 a 47 35 24 6 158 0 0 1 0 160 8 12 24 23 67 47 34 c 34 44 86 142 0 0 0 0 159 0 12 18 35 37 24 39 52 g 41 46 26 5 0 160 159 1 0 0 136 122 27 26 45 39 42 t 38 35 24 7 2 0 1 158 1 0 4 8 74 74 24 35 32

positions_6nt_m1_shift0 (positions_6nt_m1) 0.812 0.638 11.055 0.638 0.908 2.066 0.906 25 33 4 21 34 22 33 24.571 27
; oligos_6nt_mkv4_m4 versus positions_6nt_m1; m=3/8; ncol2=14; w=11; offset=-2; strand=D; shift=0; score=24.5714; byCCAGGTCACasw--- ; cor=0.812; Ncor=0.638; logoDP=11.055; NIcor=0.638; NsEucl=0.908; SSD=2.066; NSW=0.906; rcor=25; rNcor=33; rlogoDP=4; rNIcor=21; rNsEucl=34; rSSD=22; rNSW=33; rank_mean=24.571; match_rank=27 a 56 38 22 54 254 0 0 0 0 256 4 172 46 75 0 0 0 c 70 96 185 184 1 2 0 0 256 0 229 28 75 56 0 0 0 g 64 53 21 7 1 254 256 0 0 0 12 20 76 58 0 0 0 t 66 69 28 11 0 0 0 256 0 0 11 36 59 67 0 0 0

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc) 0.838 0.659 4.125 0.192 0.914 1.771 0.919 20 30 32 36 32 20 25 27.857 31
; oligos_6nt_mkv4_m4 versus positions_6nt_m2_rc; m=4/8; ncol2=14; w=11; offset=-2; strand=R; shift=0; score=27.8571; gvCCAGGTCATGgt--- ; cor=0.838; Ncor=0.659; logoDP=4.125; NIcor=0.192; NsEucl=0.914; SSD=1.771; NSW=0.919; rcor=20; rNcor=30; rlogoDP=32; rNIcor=36; rNsEucl=32; rSSD=20; rNSW=25; rank_mean=27.857; match_rank=31 a 51 52 14 30 203 0 1 0 0 205 14 16 49 46 0 0 0 c 51 55 156 163 0 0 0 0 205 0 14 19 50 51 0 0 0 g 61 53 17 1 2 204 204 0 0 0 32 153 61 34 0 0 0 t 42 45 18 11 0 1 0 205 0 0 145 17 45 74 0 0 0

positions_7nt_m5_shift0 (positions_7nt_m5) 0.795 0.624 8.762 0.615 0.905 2.193 0.900 32 34 19 22 35 25 34 28.714 32
; oligos_6nt_mkv4_m4 versus positions_7nt_m5; m=5/8; ncol2=14; w=11; offset=-2; strand=D; shift=0; score=28.7143; kbCCAGGTCAAGgt--- ; cor=0.795; Ncor=0.624; logoDP=8.762; NIcor=0.615; NsEucl=0.905; SSD=2.193; NSW=0.900; rcor=32; rNcor=34; rlogoDP=19; rNIcor=22; rNsEucl=35; rSSD=25; rNSW=34; rank_mean=28.714; match_rank=32 a 61 53 20 32 253 4 5 4 1 251 198 17 61 63 0 0 0 c 51 75 212 228 5 3 0 5 252 11 18 11 54 65 0 0 0 g 74 67 15 1 3 254 254 5 7 1 33 229 89 50 0 0 0 t 80 71 19 5 5 5 7 252 6 3 17 9 62 88 0 0 0

positions_7nt_m3_shift0 (positions_7nt_m3) 0.791 0.580 9.316 0.573 0.903 2.267 0.897 35 37 14 23 36 28 35 29.714 34
; oligos_6nt_mkv4_m4 versus positions_7nt_m3; m=6/8; ncol2=15; w=11; offset=-2; strand=D; shift=0; score=29.7143; smCCAGGTCATGcyg-- ; cor=0.791; Ncor=0.580; logoDP=9.316; NIcor=0.573; NsEucl=0.903; SSD=2.267; NSW=0.897; rcor=35; rNcor=37; rlogoDP=14; rNIcor=23; rNsEucl=36; rSSD=28; rNSW=35; rank_mean=29.714; match_rank=34 a 44 53 13 15 186 0 3 2 3 192 6 13 41 42 45 0 0 c 54 54 154 175 1 0 0 3 191 3 14 18 85 51 33 0 0 g 52 43 15 1 4 195 191 5 3 0 16 149 37 31 74 0 0 t 48 48 16 7 7 3 4 188 1 3 162 18 35 74 46 0 0

positions_7nt_m1_shift0 (positions_7nt_m1) 0.771 0.565 8.799 0.554 0.899 2.473 0.888 37 38 18 25 37 35 36 32.286 37
; oligos_6nt_mkv4_m4 versus positions_7nt_m1; m=7/8; ncol2=15; w=11; offset=-2; strand=D; shift=0; score=32.2857; byCCAGGTCACCtkg-- ; cor=0.771; Ncor=0.565; logoDP=8.799; NIcor=0.554; NsEucl=0.899; SSD=2.473; NSW=0.888; rcor=37; rNcor=38; rlogoDP=18; rNIcor=25; rNsEucl=37; rSSD=35; rNSW=36; rank_mean=32.286; match_rank=37 a 63 54 14 13 282 3 3 6 6 273 5 32 53 54 67 0 0 c 79 94 235 262 2 5 5 5 275 4 254 210 68 66 72 0 0 g 74 64 18 6 4 279 281 10 6 10 15 17 57 80 109 0 0 t 75 79 24 10 3 4 2 270 4 4 17 32 113 91 43 0 0

positions_7nt_m2_shift0 (positions_7nt_m2) 0.755 0.554 8.505 0.540 0.895 2.650 0.880 39 39 22 26 39 37 39 34.429 39
; oligos_6nt_mkv4_m4 versus positions_7nt_m2; m=8/8; ncol2=15; w=11; offset=-2; strand=D; shift=0; score=34.4286; byCAAGGTCACCttg-- ; cor=0.755; Ncor=0.554; logoDP=8.505; NIcor=0.540; NsEucl=0.895; SSD=2.650; NSW=0.880; rcor=39; rNcor=39; rlogoDP=22; rNIcor=26; rNsEucl=39; rSSD=37; rNSW=39; rank_mean=34.429; match_rank=39 a 55 60 17 301 305 8 6 3 5 322 9 56 83 76 63 0 0 c 87 122 293 18 4 3 1 6 307 2 299 241 78 76 64 0 0 g 101 56 9 7 17 314 327 5 19 6 13 19 45 81 147 0 0 t 93 98 17 10 10 11 2 322 5 6 15 20 130 103 62 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4)																	; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=11; shift=2; ncol=17; --cvAGGTCAGsg---- ; Alignment reference a 0 0 226 281 963 0 0 0 0 961 15 236 236 0 0 0 0 c 0 0 281 294 9 10 0 1 977 3 93 253 211 0 0 0 0 g 0 0 231 275 4 967 977 1 0 12 821 340 327 0 0 0 0 t 0 0 239 127 1 0 0 975 0 1 48 148 203 0 0 0 0
positions_7nt_m4_shift0 (positions_7nt_m4)	0.903	0.662	9.289	0.648	0.934	1.068	0.951	8	29	15	19	17	7	12	15.286	13	; oligos_6nt_mkv4_m4 versus positions_7nt_m4; m=1/8; ncol2=15; w=11; offset=-2; strand=D; shift=0; score=15.2857; ssCCAGGTCAGGgcr-- ; cor=0.903; Ncor=0.662; logoDP=9.289; NIcor=0.648; NsEucl=0.934; SSD=1.068; NSW=0.951; rcor=8; rNcor=29; rlogoDP=15; rNIcor=19; rNsEucl=17; rSSD=7; rNSW=12; rank_mean=15.286; match_rank=13 a 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 0 0 c 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 0 0 g 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 0 0 t 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64 0 0
positions_6nt_m4_rc_shift0 (positions_6nt_m4_rc)	0.922	0.597	3.908	0.102	0.939	0.896	0.959	5	36	37	39	15	5	6	20.429	21	; oligos_6nt_mkv4_m4 versus positions_6nt_m4_rc; m=2/8; ncol2=17; w=11; offset=-2; strand=R; shift=0; score=20.4286; rscCAGGTCAGGttras ; cor=0.922; Ncor=0.597; logoDP=3.908; NIcor=0.102; NsEucl=0.939; SSD=0.896; NSW=0.959; rcor=5; rNcor=36; rlogoDP=37; rNIcor=39; rNsEucl=15; rSSD=5; rNSW=6; rank_mean=20.429; match_rank=21 a 47 35 24 6 158 0 0 1 0 160 8 12 24 23 67 47 34 c 34 44 86 142 0 0 0 0 159 0 12 18 35 37 24 39 52 g 41 46 26 5 0 160 159 1 0 0 136 122 27 26 45 39 42 t 38 35 24 7 2 0 1 158 1 0 4 8 74 74 24 35 32
positions_6nt_m1_shift0 (positions_6nt_m1)	0.812	0.638	11.055	0.638	0.908	2.066	0.906	25	33	4	21	34	22	33	24.571	27	; oligos_6nt_mkv4_m4 versus positions_6nt_m1; m=3/8; ncol2=14; w=11; offset=-2; strand=D; shift=0; score=24.5714; byCCAGGTCACasw--- ; cor=0.812; Ncor=0.638; logoDP=11.055; NIcor=0.638; NsEucl=0.908; SSD=2.066; NSW=0.906; rcor=25; rNcor=33; rlogoDP=4; rNIcor=21; rNsEucl=34; rSSD=22; rNSW=33; rank_mean=24.571; match_rank=27 a 56 38 22 54 254 0 0 0 0 256 4 172 46 75 0 0 0 c 70 96 185 184 1 2 0 0 256 0 229 28 75 56 0 0 0 g 64 53 21 7 1 254 256 0 0 0 12 20 76 58 0 0 0 t 66 69 28 11 0 0 0 256 0 0 11 36 59 67 0 0 0
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)	0.838	0.659	4.125	0.192	0.914	1.771	0.919	20	30	32	36	32	20	25	27.857	31	; oligos_6nt_mkv4_m4 versus positions_6nt_m2_rc; m=4/8; ncol2=14; w=11; offset=-2; strand=R; shift=0; score=27.8571; gvCCAGGTCATGgt--- ; cor=0.838; Ncor=0.659; logoDP=4.125; NIcor=0.192; NsEucl=0.914; SSD=1.771; NSW=0.919; rcor=20; rNcor=30; rlogoDP=32; rNIcor=36; rNsEucl=32; rSSD=20; rNSW=25; rank_mean=27.857; match_rank=31 a 51 52 14 30 203 0 1 0 0 205 14 16 49 46 0 0 0 c 51 55 156 163 0 0 0 0 205 0 14 19 50 51 0 0 0 g 61 53 17 1 2 204 204 0 0 0 32 153 61 34 0 0 0 t 42 45 18 11 0 1 0 205 0 0 145 17 45 74 0 0 0
positions_7nt_m5_shift0 (positions_7nt_m5)	0.795	0.624	8.762	0.615	0.905	2.193	0.900	32	34	19	22	35	25	34	28.714	32	; oligos_6nt_mkv4_m4 versus positions_7nt_m5; m=5/8; ncol2=14; w=11; offset=-2; strand=D; shift=0; score=28.7143; kbCCAGGTCAAGgt--- ; cor=0.795; Ncor=0.624; logoDP=8.762; NIcor=0.615; NsEucl=0.905; SSD=2.193; NSW=0.900; rcor=32; rNcor=34; rlogoDP=19; rNIcor=22; rNsEucl=35; rSSD=25; rNSW=34; rank_mean=28.714; match_rank=32 a 61 53 20 32 253 4 5 4 1 251 198 17 61 63 0 0 0 c 51 75 212 228 5 3 0 5 252 11 18 11 54 65 0 0 0 g 74 67 15 1 3 254 254 5 7 1 33 229 89 50 0 0 0 t 80 71 19 5 5 5 7 252 6 3 17 9 62 88 0 0 0
positions_7nt_m3_shift0 (positions_7nt_m3)	0.791	0.580	9.316	0.573	0.903	2.267	0.897	35	37	14	23	36	28	35	29.714	34	; oligos_6nt_mkv4_m4 versus positions_7nt_m3; m=6/8; ncol2=15; w=11; offset=-2; strand=D; shift=0; score=29.7143; smCCAGGTCATGcyg-- ; cor=0.791; Ncor=0.580; logoDP=9.316; NIcor=0.573; NsEucl=0.903; SSD=2.267; NSW=0.897; rcor=35; rNcor=37; rlogoDP=14; rNIcor=23; rNsEucl=36; rSSD=28; rNSW=35; rank_mean=29.714; match_rank=34 a 44 53 13 15 186 0 3 2 3 192 6 13 41 42 45 0 0 c 54 54 154 175 1 0 0 3 191 3 14 18 85 51 33 0 0 g 52 43 15 1 4 195 191 5 3 0 16 149 37 31 74 0 0 t 48 48 16 7 7 3 4 188 1 3 162 18 35 74 46 0 0
positions_7nt_m1_shift0 (positions_7nt_m1)	0.771	0.565	8.799	0.554	0.899	2.473	0.888	37	38	18	25	37	35	36	32.286	37	; oligos_6nt_mkv4_m4 versus positions_7nt_m1; m=7/8; ncol2=15; w=11; offset=-2; strand=D; shift=0; score=32.2857; byCCAGGTCACCtkg-- ; cor=0.771; Ncor=0.565; logoDP=8.799; NIcor=0.554; NsEucl=0.899; SSD=2.473; NSW=0.888; rcor=37; rNcor=38; rlogoDP=18; rNIcor=25; rNsEucl=37; rSSD=35; rNSW=36; rank_mean=32.286; match_rank=37 a 63 54 14 13 282 3 3 6 6 273 5 32 53 54 67 0 0 c 79 94 235 262 2 5 5 5 275 4 254 210 68 66 72 0 0 g 74 64 18 6 4 279 281 10 6 10 15 17 57 80 109 0 0 t 75 79 24 10 3 4 2 270 4 4 17 32 113 91 43 0 0
positions_7nt_m2_shift0 (positions_7nt_m2)	0.755	0.554	8.505	0.540	0.895	2.650	0.880	39	39	22	26	39	37	39	34.429	39	; oligos_6nt_mkv4_m4 versus positions_7nt_m2; m=8/8; ncol2=15; w=11; offset=-2; strand=D; shift=0; score=34.4286; byCAAGGTCACCttg-- ; cor=0.755; Ncor=0.554; logoDP=8.505; NIcor=0.540; NsEucl=0.895; SSD=2.650; NSW=0.880; rcor=39; rNcor=39; rlogoDP=22; rNIcor=26; rNsEucl=39; rSSD=37; rNSW=39; rank_mean=34.429; match_rank=39 a 55 60 17 301 305 8 6 3 5 322 9 56 83 76 63 0 0 c 87 122 293 18 4 3 1 6 307 2 299 241 78 76 64 0 0 g 101 56 9 7 17 314 327 5 19 6 13 19 45 81 147 0 0 t 93 98 17 10 10 11 2 322 5 6 15 20 130 103 62 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift1 ; 2 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=10; shift=1; ncol=13; -waATGTCAkw-- ; Alignment reference a 0 562 707 1681 0 0 0 0 1681 394 446 0 0 c 0 356 407 0 0 0 0 1681 0 401 410 0 0 g 0 311 290 0 0 1681 0 0 0 434 392 0 0 t 0 452 277 0 1681 0 1681 0 0 452 433 0 0

positions_6nt_m5_shift0 (positions_6nt_m5) 0.886 0.682 8.811 0.667 0.925 1.131 0.943 14 28 17 18 25 8 17 18.143 16
; oligos_6nt_mkv4_m1 versus positions_6nt_m5; m=1/1; ncol2=13; w=10; offset=-1; strand=D; shift=0; score=18.1429; wwAATGTCATGwy ; cor=0.886; Ncor=0.682; logoDP=8.811; NIcor=0.667; NsEucl=0.925; SSD=1.131; NSW=0.943; rcor=14; rNcor=28; rlogoDP=17; rNIcor=18; rNsEucl=25; rSSD=8; rNSW=17; rank_mean=18.143; match_rank=16 a 127 136 335 387 8 9 13 10 395 18 45 135 102 c 66 70 28 7 1 3 7 384 6 14 27 66 111 g 80 60 27 9 8 402 2 11 7 14 319 75 73 t 144 151 27 14 400 3 395 12 9 371 26 141 131

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m1_shift1 (oligos_6nt_mkv4_m1)																		; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=10; shift=1; ncol=13; -waATGTCAkw-- ; Alignment reference a 0 562 707 1681 0 0 0 0 1681 394 446 0 0 c 0 356 407 0 0 0 0 1681 0 401 410 0 0 g 0 311 290 0 0 1681 0 0 0 434 392 0 0 t 0 452 277 0 1681 0 1681 0 0 452 433 0 0
positions_6nt_m5_shift0 (positions_6nt_m5)		0.886	0.682	8.811	0.667	0.925	1.131	0.943	14	28	17	18	25	8	17	18.143	16	; oligos_6nt_mkv4_m1 versus positions_6nt_m5; m=1/1; ncol2=13; w=10; offset=-1; strand=D; shift=0; score=18.1429; wwAATGTCATGwy ; cor=0.886; Ncor=0.682; logoDP=8.811; NIcor=0.667; NsEucl=0.925; SSD=1.131; NSW=0.943; rcor=14; rNcor=28; rlogoDP=17; rNIcor=18; rNsEucl=25; rSSD=8; rNSW=17; rank_mean=18.143; match_rank=16 a 127 136 335 387 8 9 13 10 395 18 45 135 102 c 66 70 28 7 1 3 7 384 6 14 27 66 111 g 80 60 27 9 8 402 2 11 7 14 319 75 73 t 144 151 27 14 400 3 395 12 9 371 26 141 131

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=19; shift=0; ncol=19; ssGCCCAGGGCAsGGGGsg ; Alignment reference a 2 2 0 0 0 0 10 0 0 0 0 10 0 1 0 1 1 2 2 c 6 5 2 10 9 11 0 1 0 0 10 1 3 1 0 2 1 5 2 g 3 3 9 1 2 0 1 10 10 11 1 0 7 9 11 8 8 4 6 t 0 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 1 0 1

dyads_m5_rc_shift0 (dyads_m5_rc) 0.827 0.827 10.599 0.447 0.933 3.216 0.915 22 13 6 27 18 38 29 21.857 24
; dyads_m3 versus dyads_m5_rc; m=1/2; ncol2=19; w=19; offset=0; strand=R; shift=0; score=21.8571; bbGCCCRGGSSYSGSGSmG ; cor=0.827; Ncor=0.827; logoDP=10.599; NIcor=0.447; NsEucl=0.933; SSD=3.216; NSW=0.915; rcor=22; rNcor=13; rlogoDP=6; rNIcor=27; rNsEucl=18; rSSD=38; rNSW=29; rank_mean=21.857; match_rank=24 a 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 2 0 c 1 1 0 4 4 4 0 0 0 1 3 1 1 0 1 0 1 2 0 g 1 2 4 0 0 0 1 4 4 3 1 0 3 4 3 4 3 0 4 t 2 1 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0

positions_7nt_m4_shift2 (positions_7nt_m4) 0.756 0.597 8.077 0.569 0.912 3.488 0.884 38 35 27 24 33 39 37 33.286 38
; dyads_m3 versus positions_7nt_m4; m=2/2; ncol2=15; w=15; offset=2; strand=D; shift=2; score=33.2857; --ssCCAGGTCAGGgcr-- ; cor=0.756; Ncor=0.597; logoDP=8.077; NIcor=0.569; NsEucl=0.912; SSD=3.488; NSW=0.884; rcor=38; rNcor=35; rlogoDP=27; rNIcor=24; rNsEucl=33; rSSD=39; rNSW=37; rank_mean=33.286; match_rank=38 a 0 0 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 0 0 c 0 0 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 0 0 g 0 0 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 0 0 t 0 0 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64 0 0