One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/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/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: local_words_7nt_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
local_words_7nt_m1_shift0 (local_words_7nt_m1)
; local_words_7nt_m1; m=0 (reference); ncol1=21; shift=0; ncol=21; wbwCATTTcchgkAAATGtat ; Alignment reference a 53 36 70 5 143 5 3 14 23 15 40 20 22 116 154 129 8 6 39 46 38 c 28 40 24 139 4 1 1 11 97 108 41 10 8 9 1 1 4 10 24 39 39 g 35 40 22 8 8 2 1 11 7 0 29 100 84 20 1 25 4 137 24 36 33 t 43 43 43 7 4 151 154 123 32 36 49 29 45 14 3 4 143 6 72 38 49

local_words_7nt_m3_shift0 (local_words_7nt_m3) 0.969 0.969 7.137 0.970 0.979 0.382 0.991 1 1 8 1 1 1 1 2.000 1
; local_words_7nt_m1 versus local_words_7nt_m3; m=1/7; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 2; kdaCATTTyCmrgaAATGtmw ; cor=0.969; Ncor=0.969; logoDP=7.137; NIcor=0.970; NsEucl=0.979; SSD=0.382; NSW=0.991; rcor=1; rNcor=1; rlogoDP=8; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.000; match_rank=1 a 38 43 81 8 142 9 3 13 24 22 40 68 25 103 157 154 13 10 36 48 40 c 26 35 15 136 4 5 3 5 85 112 75 13 7 11 0 3 9 11 17 40 36 g 43 41 27 6 6 8 0 10 8 0 10 65 96 34 2 1 9 127 21 37 32 t 53 41 37 10 8 138 154 132 43 26 35 14 32 12 1 2 129 12 86 35 52

local_words_7nt_m2_shift0 (local_words_7nt_m2) 0.963 0.963 6.461 0.954 0.977 0.457 0.989 4 2 9 2 2 4 2 3.571 2
; local_words_7nt_m1 versus local_words_7nt_m2; m=2/7; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 3.5714; awaCATTTcybgkaaATGtaw ; cor=0.963; Ncor=0.963; logoDP=6.461; NIcor=0.954; NsEucl=0.977; SSD=0.457; NSW=0.989; rcor=4; rNcor=2; rlogoDP=9; rNIcor=2; rNsEucl=2; rSSD=4; rNSW=2; rank_mean=3.571; match_rank=2 a 36 33 74 5 114 3 2 4 15 15 17 19 18 83 81 91 9 4 30 39 34 c 28 23 15 105 4 2 1 2 70 62 41 21 3 10 11 7 4 6 16 28 24 g 30 26 14 8 3 3 0 0 10 5 34 69 50 21 19 5 2 111 10 27 25 t 31 43 22 7 4 117 122 119 30 43 33 16 54 11 14 22 110 4 69 31 42

positions_7nt_m2_rc_shift0 (positions_7nt_m2_rc) 0.824 0.824 6.141 0.786 0.949 2.271 0.946 15 8 11 8 13 16 15 12.286 12
; local_words_7nt_m1 versus positions_7nt_m2_rc; m=3/7; ncol2=21; w=21; offset=0; strand=R; shift=0; score=12.2857; ysTsATTTCygGGAAatsAsh ; cor=0.824; Ncor=0.824; logoDP=6.141; NIcor=0.786; NsEucl=0.949; SSD=2.271; NSW=0.946; rcor=15; rNcor=8; rlogoDP=11; rNIcor=8; rNsEucl=13; rSSD=16; rNSW=15; rank_mean=12.286; match_rank=12 a 64 52 22 14 199 10 0 0 17 2 61 25 47 257 254 176 45 16 189 63 69 c 68 73 29 137 17 8 4 46 241 132 7 2 3 2 1 15 47 105 23 77 68 g 57 72 22 102 24 12 1 4 1 4 143 226 200 0 3 56 41 129 23 72 57 t 71 63 187 7 20 230 255 210 1 122 49 7 10 1 2 13 127 10 25 48 66

positions_7nt_m1_rc_shift0 (positions_7nt_m1_rc) 0.814 0.814 5.915 0.768 0.948 2.341 0.944 16 9 13 9 14 17 16 13.429 15
; local_words_7nt_m1 versus positions_7nt_m1_rc; m=4/7; ncol2=21; w=21; offset=0; strand=R; shift=0; score=13.4286; tsTsatTTCCwGGAAAysAsw ; cor=0.814; Ncor=0.814; logoDP=5.915; NIcor=0.768; NsEucl=0.948; SSD=2.341; NSW=0.944; rcor=16; rNcor=9; rlogoDP=13; rNIcor=9; rNsEucl=14; rSSD=17; rNSW=16; rank_mean=13.429; match_rank=15 a 116 96 46 27 289 62 2 2 47 7 142 28 4 446 479 334 27 35 340 91 131 c 113 131 51 244 23 105 2 2 400 395 97 3 2 6 2 19 137 247 53 148 112 g 117 143 57 196 87 30 3 8 4 2 92 442 401 28 2 113 31 167 39 138 117 t 138 114 330 17 85 287 477 472 33 80 153 11 77 4 1 18 289 35 52 107 124

positions_7nt_m3_shift3 (positions_7nt_m3) 0.805 0.613 5.774 0.554 0.932 2.345 0.927 18 16 16 15 19 18 19 17.286 18
; local_words_7nt_m1 versus positions_7nt_m3; m=5/7; ncol2=16; w=16; offset=3; strand=D; shift=3; score=17.2857; ---srTTTCYwGGAArtsr-- ; cor=0.805; Ncor=0.613; logoDP=5.774; NIcor=0.554; NsEucl=0.932; SSD=2.345; NSW=0.927; rcor=18; rNcor=16; rlogoDP=16; rNIcor=15; rNsEucl=19; rSSD=18; rNSW=19; rank_mean=17.286; match_rank=18 a 0 0 0 225 433 191 3 3 105 1 380 30 39 1231 1228 634 142 240 404 0 0 c 0 0 0 372 246 86 4 3 1125 892 153 7 2 2 3 44 216 326 279 0 0 g 0 0 0 375 329 66 7 2 3 1 306 1196 1157 1 2 411 156 453 317 0 0 t 0 0 0 265 229 894 1223 1229 4 343 398 4 39 3 4 148 723 218 237 0 0

oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1) 0.813 0.542 6.083 0.495 0.927 2.108 0.925 17 21 12 17 21 15 21 17.714 19
; local_words_7nt_m1 versus oligos_7nt_mkv4_m1; m=6/7; ncol2=14; w=14; offset=3; strand=D; shift=3; score=17.7143; ---srTTTCCwGGAAay---- ; cor=0.813; Ncor=0.542; logoDP=6.083; NIcor=0.495; NsEucl=0.927; SSD=2.108; NSW=0.925; rcor=17; rNcor=21; rlogoDP=12; rNIcor=17; rNsEucl=21; rSSD=15; rNSW=21; rank_mean=17.714; match_rank=19 a 0 0 0 237 426 84 1 1 178 0 456 265 0 1319 1318 550 257 0 0 0 0 c 0 0 0 455 268 57 1 40 1142 1320 266 1 0 0 2 202 358 0 0 0 0 g 0 0 0 349 370 74 0 0 0 0 176 1054 1138 0 0 315 228 0 0 0 0 t 0 0 0 279 256 1105 1318 1279 0 0 422 0 182 1 0 253 477 0 0 0 0

oligos_7nt_mkv4_m3_rc_shift4 (oligos_7nt_mkv4_m3_rc) 0.755 0.467 5.502 0.418 0.911 2.659 0.898 24 24 19 20 24 22 24 22.429 24
; local_words_7nt_m1 versus oligos_7nt_mkv4_m3_rc; m=7/7; ncol2=13; w=13; offset=4; strand=R; shift=4; score=22.4286; ----ryTTCykGGAAry---- ; cor=0.755; Ncor=0.467; logoDP=5.502; NIcor=0.418; NsEucl=0.911; SSD=2.659; NSW=0.898; rcor=24; rNcor=24; rlogoDP=19; rNIcor=20; rNsEucl=24; rSSD=22; rNSW=24; rank_mean=22.429; match_rank=24 a 0 0 0 0 388 209 0 3 23 0 0 0 43 1214 1216 497 230 0 0 0 0 c 0 0 0 0 244 333 0 0 1195 768 10 4 0 1 3 158 337 0 0 0 0 g 0 0 0 0 354 185 2 3 0 1 612 1214 1168 0 0 347 271 0 0 0 0 t 0 0 0 0 233 492 1217 1213 1 450 597 1 8 4 0 217 381 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
local_words_7nt_m1_shift0 (local_words_7nt_m1)																	; local_words_7nt_m1; m=0 (reference); ncol1=21; shift=0; ncol=21; wbwCATTTcchgkAAATGtat ; Alignment reference a 53 36 70 5 143 5 3 14 23 15 40 20 22 116 154 129 8 6 39 46 38 c 28 40 24 139 4 1 1 11 97 108 41 10 8 9 1 1 4 10 24 39 39 g 35 40 22 8 8 2 1 11 7 0 29 100 84 20 1 25 4 137 24 36 33 t 43 43 43 7 4 151 154 123 32 36 49 29 45 14 3 4 143 6 72 38 49
local_words_7nt_m3_shift0 (local_words_7nt_m3)	0.969	0.969	7.137	0.970	0.979	0.382	0.991	1	1	8	1	1	1	1	2.000	1	; local_words_7nt_m1 versus local_words_7nt_m3; m=1/7; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 2; kdaCATTTyCmrgaAATGtmw ; cor=0.969; Ncor=0.969; logoDP=7.137; NIcor=0.970; NsEucl=0.979; SSD=0.382; NSW=0.991; rcor=1; rNcor=1; rlogoDP=8; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.000; match_rank=1 a 38 43 81 8 142 9 3 13 24 22 40 68 25 103 157 154 13 10 36 48 40 c 26 35 15 136 4 5 3 5 85 112 75 13 7 11 0 3 9 11 17 40 36 g 43 41 27 6 6 8 0 10 8 0 10 65 96 34 2 1 9 127 21 37 32 t 53 41 37 10 8 138 154 132 43 26 35 14 32 12 1 2 129 12 86 35 52
local_words_7nt_m2_shift0 (local_words_7nt_m2)	0.963	0.963	6.461	0.954	0.977	0.457	0.989	4	2	9	2	2	4	2	3.571	2	; local_words_7nt_m1 versus local_words_7nt_m2; m=2/7; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 3.5714; awaCATTTcybgkaaATGtaw ; cor=0.963; Ncor=0.963; logoDP=6.461; NIcor=0.954; NsEucl=0.977; SSD=0.457; NSW=0.989; rcor=4; rNcor=2; rlogoDP=9; rNIcor=2; rNsEucl=2; rSSD=4; rNSW=2; rank_mean=3.571; match_rank=2 a 36 33 74 5 114 3 2 4 15 15 17 19 18 83 81 91 9 4 30 39 34 c 28 23 15 105 4 2 1 2 70 62 41 21 3 10 11 7 4 6 16 28 24 g 30 26 14 8 3 3 0 0 10 5 34 69 50 21 19 5 2 111 10 27 25 t 31 43 22 7 4 117 122 119 30 43 33 16 54 11 14 22 110 4 69 31 42
positions_7nt_m2_rc_shift0 (positions_7nt_m2_rc)	0.824	0.824	6.141	0.786	0.949	2.271	0.946	15	8	11	8	13	16	15	12.286	12	; local_words_7nt_m1 versus positions_7nt_m2_rc; m=3/7; ncol2=21; w=21; offset=0; strand=R; shift=0; score=12.2857; ysTsATTTCygGGAAatsAsh ; cor=0.824; Ncor=0.824; logoDP=6.141; NIcor=0.786; NsEucl=0.949; SSD=2.271; NSW=0.946; rcor=15; rNcor=8; rlogoDP=11; rNIcor=8; rNsEucl=13; rSSD=16; rNSW=15; rank_mean=12.286; match_rank=12 a 64 52 22 14 199 10 0 0 17 2 61 25 47 257 254 176 45 16 189 63 69 c 68 73 29 137 17 8 4 46 241 132 7 2 3 2 1 15 47 105 23 77 68 g 57 72 22 102 24 12 1 4 1 4 143 226 200 0 3 56 41 129 23 72 57 t 71 63 187 7 20 230 255 210 1 122 49 7 10 1 2 13 127 10 25 48 66
positions_7nt_m1_rc_shift0 (positions_7nt_m1_rc)	0.814	0.814	5.915	0.768	0.948	2.341	0.944	16	9	13	9	14	17	16	13.429	15	; local_words_7nt_m1 versus positions_7nt_m1_rc; m=4/7; ncol2=21; w=21; offset=0; strand=R; shift=0; score=13.4286; tsTsatTTCCwGGAAAysAsw ; cor=0.814; Ncor=0.814; logoDP=5.915; NIcor=0.768; NsEucl=0.948; SSD=2.341; NSW=0.944; rcor=16; rNcor=9; rlogoDP=13; rNIcor=9; rNsEucl=14; rSSD=17; rNSW=16; rank_mean=13.429; match_rank=15 a 116 96 46 27 289 62 2 2 47 7 142 28 4 446 479 334 27 35 340 91 131 c 113 131 51 244 23 105 2 2 400 395 97 3 2 6 2 19 137 247 53 148 112 g 117 143 57 196 87 30 3 8 4 2 92 442 401 28 2 113 31 167 39 138 117 t 138 114 330 17 85 287 477 472 33 80 153 11 77 4 1 18 289 35 52 107 124
positions_7nt_m3_shift3 (positions_7nt_m3)	0.805	0.613	5.774	0.554	0.932	2.345	0.927	18	16	16	15	19	18	19	17.286	18	; local_words_7nt_m1 versus positions_7nt_m3; m=5/7; ncol2=16; w=16; offset=3; strand=D; shift=3; score=17.2857; ---srTTTCYwGGAArtsr-- ; cor=0.805; Ncor=0.613; logoDP=5.774; NIcor=0.554; NsEucl=0.932; SSD=2.345; NSW=0.927; rcor=18; rNcor=16; rlogoDP=16; rNIcor=15; rNsEucl=19; rSSD=18; rNSW=19; rank_mean=17.286; match_rank=18 a 0 0 0 225 433 191 3 3 105 1 380 30 39 1231 1228 634 142 240 404 0 0 c 0 0 0 372 246 86 4 3 1125 892 153 7 2 2 3 44 216 326 279 0 0 g 0 0 0 375 329 66 7 2 3 1 306 1196 1157 1 2 411 156 453 317 0 0 t 0 0 0 265 229 894 1223 1229 4 343 398 4 39 3 4 148 723 218 237 0 0
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)	0.813	0.542	6.083	0.495	0.927	2.108	0.925	17	21	12	17	21	15	21	17.714	19	; local_words_7nt_m1 versus oligos_7nt_mkv4_m1; m=6/7; ncol2=14; w=14; offset=3; strand=D; shift=3; score=17.7143; ---srTTTCCwGGAAay---- ; cor=0.813; Ncor=0.542; logoDP=6.083; NIcor=0.495; NsEucl=0.927; SSD=2.108; NSW=0.925; rcor=17; rNcor=21; rlogoDP=12; rNIcor=17; rNsEucl=21; rSSD=15; rNSW=21; rank_mean=17.714; match_rank=19 a 0 0 0 237 426 84 1 1 178 0 456 265 0 1319 1318 550 257 0 0 0 0 c 0 0 0 455 268 57 1 40 1142 1320 266 1 0 0 2 202 358 0 0 0 0 g 0 0 0 349 370 74 0 0 0 0 176 1054 1138 0 0 315 228 0 0 0 0 t 0 0 0 279 256 1105 1318 1279 0 0 422 0 182 1 0 253 477 0 0 0 0
oligos_7nt_mkv4_m3_rc_shift4 (oligos_7nt_mkv4_m3_rc)	0.755	0.467	5.502	0.418	0.911	2.659	0.898	24	24	19	20	24	22	24	22.429	24	; local_words_7nt_m1 versus oligos_7nt_mkv4_m3_rc; m=7/7; ncol2=13; w=13; offset=4; strand=R; shift=4; score=22.4286; ----ryTTCykGGAAry---- ; cor=0.755; Ncor=0.467; logoDP=5.502; NIcor=0.418; NsEucl=0.911; SSD=2.659; NSW=0.898; rcor=24; rNcor=24; rlogoDP=19; rNIcor=20; rNsEucl=24; rSSD=22; rNSW=24; rank_mean=22.429; match_rank=24 a 0 0 0 0 388 209 0 3 23 0 0 0 43 1214 1216 497 230 0 0 0 0 c 0 0 0 0 244 333 0 0 1195 768 10 4 0 1 3 158 337 0 0 0 0 g 0 0 0 0 354 185 2 3 0 1 612 1214 1168 0 0 347 271 0 0 0 0 t 0 0 0 0 233 492 1217 1213 1 450 597 1 8 4 0 217 381 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift3 ; 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
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=14; shift=3; ncol=21; ---srTTTCCwGGAAay---- ; Alignment reference a 0 0 0 237 426 84 1 1 178 0 456 265 0 1319 1318 550 257 0 0 0 0 c 0 0 0 455 268 57 1 40 1142 1320 266 1 0 0 2 202 358 0 0 0 0 g 0 0 0 349 370 74 0 0 0 0 176 1054 1138 0 0 315 228 0 0 0 0 t 0 0 0 279 256 1105 1318 1279 0 0 422 0 182 1 0 253 477 0 0 0 0

positions_7nt_m3_shift3 (positions_7nt_m3) 0.966 0.846 10.644 0.844 0.968 0.390 0.986 2 6 2 6 5 2 3 3.714 3
; oligos_7nt_mkv4_m1 versus positions_7nt_m3; m=1/4; ncol2=16; w=14; offset=0; strand=D; shift=3; score= 3.7143; ---srTTTCYwGGAArtsr-- ; cor=0.966; Ncor=0.846; logoDP=10.644; NIcor=0.844; NsEucl=0.968; SSD=0.390; NSW=0.986; rcor=2; rNcor=6; rlogoDP=2; rNIcor=6; rNsEucl=5; rSSD=2; rNSW=3; rank_mean=3.714; match_rank=3 a 0 0 0 225 433 191 3 3 105 1 380 30 39 1231 1228 634 142 240 404 0 0 c 0 0 0 372 246 86 4 3 1125 892 153 7 2 2 3 44 216 326 279 0 0 g 0 0 0 375 329 66 7 2 3 1 306 1196 1157 1 2 411 156 453 317 0 0 t 0 0 0 265 229 894 1223 1229 4 343 398 4 39 3 4 148 723 218 237 0 0

oligos_7nt_mkv4_m3_shift4 (oligos_7nt_mkv4_m3) 0.947 0.879 11.578 0.881 0.958 0.608 0.977 6 5 1 5 9 6 9 5.857 4
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3; m=2/4; ncol2=13; w=13; offset=1; strand=D; shift=4; score= 5.8571; ----ryTTCCmrGAAry---- ; cor=0.947; Ncor=0.879; logoDP=11.578; NIcor=0.881; NsEucl=0.958; SSD=0.608; NSW=0.977; rcor=6; rNcor=5; rlogoDP=1; rNIcor=5; rNsEucl=9; rSSD=6; rNSW=9; rank_mean=5.857; match_rank=4 a 0 0 0 0 381 217 0 4 8 1 597 450 1 1213 1217 492 233 0 0 0 0 c 0 0 0 0 271 347 0 0 1168 1214 612 1 0 3 2 185 354 0 0 0 0 g 0 0 0 0 337 158 3 1 0 4 10 768 1195 0 0 333 244 0 0 0 0 t 0 0 0 0 230 497 1216 1214 43 0 0 0 23 3 0 209 388 0 0 0 0

positions_7nt_m1_shift0 (positions_7nt_m1) 0.963 0.642 9.650 0.644 0.967 0.421 0.985 3 15 4 12 6 3 4 6.714 7
; oligos_7nt_mkv4_m1 versus positions_7nt_m1; m=3/4; ncol2=21; w=14; offset=-3; strand=D; shift=0; score= 6.7143; wsTsrTTTCCwGGAAatsAsa ; cor=0.963; Ncor=0.642; logoDP=9.650; NIcor=0.644; NsEucl=0.967; SSD=0.421; NSW=0.985; rcor=3; rNcor=15; rlogoDP=4; rNIcor=12; rNsEucl=6; rSSD=3; rNSW=4; rank_mean=6.714; match_rank=7 a 124 107 52 35 289 18 1 4 77 11 153 80 33 472 477 287 85 17 330 114 138 c 117 138 39 167 31 113 2 28 401 442 92 2 4 8 3 30 87 196 57 143 117 g 112 148 53 247 137 19 2 6 2 3 97 395 400 2 2 105 23 244 51 131 113 t 131 91 340 35 27 334 479 446 4 28 142 7 47 2 2 62 289 27 46 96 116

positions_7nt_m2_shift0 (positions_7nt_m2) 0.898 0.599 8.852 0.587 0.945 1.178 0.958 13 18 6 13 15 13 13 13.000 13
; oligos_7nt_mkv4_m1 versus positions_7nt_m2; m=4/4; ncol2=21; w=14; offset=-3; strand=D; shift=0; score= 13; dsTsatTTCCcrGAAATsAsr ; cor=0.898; Ncor=0.599; logoDP=8.852; NIcor=0.587; NsEucl=0.945; SSD=1.178; NSW=0.958; rcor=13; rNcor=18; rlogoDP=6; rNIcor=13; rNsEucl=15; rSSD=13; rNSW=13; rank_mean=13.000; match_rank=13 a 66 48 25 10 127 13 2 1 10 7 49 122 1 210 255 230 20 7 187 63 71 c 57 72 23 129 41 56 3 0 200 226 143 4 1 4 1 12 24 102 22 72 57 g 68 77 23 105 47 15 1 2 3 2 7 132 241 46 4 8 17 137 29 73 68 t 69 63 189 16 45 176 254 257 47 25 61 2 17 0 0 10 199 14 22 52 64

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)																	; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=14; shift=3; ncol=21; ---srTTTCCwGGAAay---- ; Alignment reference a 0 0 0 237 426 84 1 1 178 0 456 265 0 1319 1318 550 257 0 0 0 0 c 0 0 0 455 268 57 1 40 1142 1320 266 1 0 0 2 202 358 0 0 0 0 g 0 0 0 349 370 74 0 0 0 0 176 1054 1138 0 0 315 228 0 0 0 0 t 0 0 0 279 256 1105 1318 1279 0 0 422 0 182 1 0 253 477 0 0 0 0
positions_7nt_m3_shift3 (positions_7nt_m3)	0.966	0.846	10.644	0.844	0.968	0.390	0.986	2	6	2	6	5	2	3	3.714	3	; oligos_7nt_mkv4_m1 versus positions_7nt_m3; m=1/4; ncol2=16; w=14; offset=0; strand=D; shift=3; score= 3.7143; ---srTTTCYwGGAArtsr-- ; cor=0.966; Ncor=0.846; logoDP=10.644; NIcor=0.844; NsEucl=0.968; SSD=0.390; NSW=0.986; rcor=2; rNcor=6; rlogoDP=2; rNIcor=6; rNsEucl=5; rSSD=2; rNSW=3; rank_mean=3.714; match_rank=3 a 0 0 0 225 433 191 3 3 105 1 380 30 39 1231 1228 634 142 240 404 0 0 c 0 0 0 372 246 86 4 3 1125 892 153 7 2 2 3 44 216 326 279 0 0 g 0 0 0 375 329 66 7 2 3 1 306 1196 1157 1 2 411 156 453 317 0 0 t 0 0 0 265 229 894 1223 1229 4 343 398 4 39 3 4 148 723 218 237 0 0
oligos_7nt_mkv4_m3_shift4 (oligos_7nt_mkv4_m3)	0.947	0.879	11.578	0.881	0.958	0.608	0.977	6	5	1	5	9	6	9	5.857	4	; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3; m=2/4; ncol2=13; w=13; offset=1; strand=D; shift=4; score= 5.8571; ----ryTTCCmrGAAry---- ; cor=0.947; Ncor=0.879; logoDP=11.578; NIcor=0.881; NsEucl=0.958; SSD=0.608; NSW=0.977; rcor=6; rNcor=5; rlogoDP=1; rNIcor=5; rNsEucl=9; rSSD=6; rNSW=9; rank_mean=5.857; match_rank=4 a 0 0 0 0 381 217 0 4 8 1 597 450 1 1213 1217 492 233 0 0 0 0 c 0 0 0 0 271 347 0 0 1168 1214 612 1 0 3 2 185 354 0 0 0 0 g 0 0 0 0 337 158 3 1 0 4 10 768 1195 0 0 333 244 0 0 0 0 t 0 0 0 0 230 497 1216 1214 43 0 0 0 23 3 0 209 388 0 0 0 0
positions_7nt_m1_shift0 (positions_7nt_m1)	0.963	0.642	9.650	0.644	0.967	0.421	0.985	3	15	4	12	6	3	4	6.714	7	; oligos_7nt_mkv4_m1 versus positions_7nt_m1; m=3/4; ncol2=21; w=14; offset=-3; strand=D; shift=0; score= 6.7143; wsTsrTTTCCwGGAAatsAsa ; cor=0.963; Ncor=0.642; logoDP=9.650; NIcor=0.644; NsEucl=0.967; SSD=0.421; NSW=0.985; rcor=3; rNcor=15; rlogoDP=4; rNIcor=12; rNsEucl=6; rSSD=3; rNSW=4; rank_mean=6.714; match_rank=7 a 124 107 52 35 289 18 1 4 77 11 153 80 33 472 477 287 85 17 330 114 138 c 117 138 39 167 31 113 2 28 401 442 92 2 4 8 3 30 87 196 57 143 117 g 112 148 53 247 137 19 2 6 2 3 97 395 400 2 2 105 23 244 51 131 113 t 131 91 340 35 27 334 479 446 4 28 142 7 47 2 2 62 289 27 46 96 116
positions_7nt_m2_shift0 (positions_7nt_m2)	0.898	0.599	8.852	0.587	0.945	1.178	0.958	13	18	6	13	15	13	13	13.000	13	; oligos_7nt_mkv4_m1 versus positions_7nt_m2; m=4/4; ncol2=21; w=14; offset=-3; strand=D; shift=0; score= 13; dsTsatTTCCcrGAAATsAsr ; cor=0.898; Ncor=0.599; logoDP=8.852; NIcor=0.587; NsEucl=0.945; SSD=1.178; NSW=0.958; rcor=13; rNcor=18; rlogoDP=6; rNIcor=13; rNsEucl=15; rSSD=13; rNSW=13; rank_mean=13.000; match_rank=13 a 66 48 25 10 127 13 2 1 10 7 49 122 1 210 255 230 20 7 187 63 71 c 57 72 23 129 41 56 3 0 200 226 143 4 1 4 1 12 24 102 22 72 57 g 68 77 23 105 47 15 1 2 3 2 7 132 241 46 4 8 17 137 29 73 68 t 69 63 189 16 45 176 254 257 47 25 61 2 17 0 0 10 199 14 22 52 64

One-to-n matrix alignment; reference matrix: positions_7nt_m1_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_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=21; shift=0; ncol=21; wsTsrTTTCCwGGAAatsAsa ; Alignment reference a 124 107 52 35 289 18 1 4 77 11 153 80 33 472 477 287 85 17 330 114 138 c 117 138 39 167 31 113 2 28 401 442 92 2 4 8 3 30 87 196 57 143 117 g 112 148 53 247 137 19 2 6 2 3 97 395 400 2 2 105 23 244 51 131 113 t 131 91 340 35 27 334 479 446 4 28 142 7 47 2 2 62 289 27 46 96 116

positions_7nt_m2_shift0 (positions_7nt_m2) 0.941 0.941 8.066 0.934 0.970 0.768 0.982 9 4 7 3 4 9 6 6.000 5
; positions_7nt_m1 versus positions_7nt_m2; m=1/2; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 6; dsTsatTTCCcrGAAATsAsr ; cor=0.941; Ncor=0.941; logoDP=8.066; NIcor=0.934; NsEucl=0.970; SSD=0.768; NSW=0.982; rcor=9; rNcor=4; rlogoDP=7; rNIcor=3; rNsEucl=4; rSSD=9; rNSW=6; rank_mean=6.000; match_rank=5 a 66 48 25 10 127 13 2 1 10 7 49 122 1 210 255 230 20 7 187 63 71 c 57 72 23 129 41 56 3 0 200 226 143 4 1 4 1 12 24 102 22 72 57 g 68 77 23 105 47 15 1 2 3 2 7 132 241 46 4 8 17 137 29 73 68 t 69 63 189 16 45 176 254 257 47 25 61 2 17 0 0 10 199 14 22 52 64

positions_7nt_m3_rc_shift2 (positions_7nt_m3_rc) 0.945 0.720 5.359 0.294 0.964 0.662 0.979 7 13 20 21 7 7 8 11.857 11
; positions_7nt_m1 versus positions_7nt_m3_rc; m=2/2; ncol2=16; w=16; offset=2; strand=R; shift=2; score=11.8571; --ysayTTCCwRGAAAys--- ; cor=0.945; Ncor=0.720; logoDP=5.359; NIcor=0.294; NsEucl=0.964; SSD=0.662; NSW=0.979; rcor=7; rNcor=13; rlogoDP=20; rNIcor=21; rNsEucl=7; rSSD=7; rNSW=8; rank_mean=11.857; match_rank=11 a 0 0 237 218 723 148 4 3 39 4 398 343 4 1229 1223 894 229 265 0 0 0 c 0 0 317 453 156 411 2 1 1157 1196 306 1 3 2 7 66 329 375 0 0 0 g 0 0 279 326 216 44 3 2 2 7 153 892 1125 3 4 86 246 372 0 0 0 t 0 0 404 240 142 634 1228 1231 39 30 380 1 105 3 3 191 433 225 0 0 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=21; shift=0; ncol=21; wsTsrTTTCCwGGAAatsAsa ; Alignment reference a 124 107 52 35 289 18 1 4 77 11 153 80 33 472 477 287 85 17 330 114 138 c 117 138 39 167 31 113 2 28 401 442 92 2 4 8 3 30 87 196 57 143 117 g 112 148 53 247 137 19 2 6 2 3 97 395 400 2 2 105 23 244 51 131 113 t 131 91 340 35 27 334 479 446 4 28 142 7 47 2 2 62 289 27 46 96 116
positions_7nt_m2_shift0 (positions_7nt_m2)	0.941	0.941	8.066	0.934	0.970	0.768	0.982	9	4	7	3	4	9	6	6.000	5	; positions_7nt_m1 versus positions_7nt_m2; m=1/2; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 6; dsTsatTTCCcrGAAATsAsr ; cor=0.941; Ncor=0.941; logoDP=8.066; NIcor=0.934; NsEucl=0.970; SSD=0.768; NSW=0.982; rcor=9; rNcor=4; rlogoDP=7; rNIcor=3; rNsEucl=4; rSSD=9; rNSW=6; rank_mean=6.000; match_rank=5 a 66 48 25 10 127 13 2 1 10 7 49 122 1 210 255 230 20 7 187 63 71 c 57 72 23 129 41 56 3 0 200 226 143 4 1 4 1 12 24 102 22 72 57 g 68 77 23 105 47 15 1 2 3 2 7 132 241 46 4 8 17 137 29 73 68 t 69 63 189 16 45 176 254 257 47 25 61 2 17 0 0 10 199 14 22 52 64
positions_7nt_m3_rc_shift2 (positions_7nt_m3_rc)	0.945	0.720	5.359	0.294	0.964	0.662	0.979	7	13	20	21	7	7	8	11.857	11	; positions_7nt_m1 versus positions_7nt_m3_rc; m=2/2; ncol2=16; w=16; offset=2; strand=R; shift=2; score=11.8571; --ysayTTCCwRGAAAys--- ; cor=0.945; Ncor=0.720; logoDP=5.359; NIcor=0.294; NsEucl=0.964; SSD=0.662; NSW=0.979; rcor=7; rNcor=13; rlogoDP=20; rNIcor=21; rNsEucl=7; rSSD=7; rNSW=8; rank_mean=11.857; match_rank=11 a 0 0 237 218 723 148 4 3 39 4 398 343 4 1229 1223 894 229 265 0 0 0 c 0 0 317 453 156 411 2 1 1157 1196 306 1 3 2 7 66 329 375 0 0 0 g 0 0 279 326 216 44 3 2 2 7 153 892 1125 3 4 86 246 372 0 0 0 t 0 0 404 240 142 634 1228 1231 39 30 380 1 105 3 3 191 433 225 0 0 0

One-to-n matrix alignment; reference matrix: local_words_7nt_m2_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
local_words_7nt_m2_shift0 (local_words_7nt_m2)
; local_words_7nt_m2; m=0 (reference); ncol1=21; shift=0; ncol=21; awaCATTTcybgkaaATGtaw ; Alignment reference a 36 33 74 5 114 3 2 4 15 15 17 19 18 83 81 91 9 4 30 39 34 c 28 23 15 105 4 2 1 2 70 62 41 21 3 10 11 7 4 6 16 28 24 g 30 26 14 8 3 3 0 0 10 5 34 69 50 21 19 5 2 111 10 27 25 t 31 43 22 7 4 117 122 119 30 43 33 16 54 11 14 22 110 4 69 31 42

local_words_7nt_m3_shift0 (local_words_7nt_m3) 0.942 0.942 5.912 0.929 0.972 0.693 0.983 8 3 14 4 3 8 5 6.429 6
; local_words_7nt_m2 versus local_words_7nt_m3; m=1/2; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 6.4286; kdaCATTTyCmrgaAATGtmw ; cor=0.942; Ncor=0.942; logoDP=5.912; NIcor=0.929; NsEucl=0.972; SSD=0.693; NSW=0.983; rcor=8; rNcor=3; rlogoDP=14; rNIcor=4; rNsEucl=3; rSSD=8; rNSW=5; rank_mean=6.429; match_rank=6 a 38 43 81 8 142 9 3 13 24 22 40 68 25 103 157 154 13 10 36 48 40 c 26 35 15 136 4 5 3 5 85 112 75 13 7 11 0 3 9 11 17 40 36 g 43 41 27 6 6 8 0 10 8 0 10 65 96 34 2 1 9 127 21 37 32 t 53 41 37 10 8 138 154 132 43 26 35 14 32 12 1 2 129 12 86 35 52

positions_7nt_m2_rc_shift0 (positions_7nt_m2_rc) 0.758 0.758 5.275 0.702 0.941 3.022 0.928 23 12 21 11 18 24 18 18.143 20
; local_words_7nt_m2 versus positions_7nt_m2_rc; m=2/2; ncol2=21; w=21; offset=0; strand=R; shift=0; score=18.1429; ysTsATTTCygGGAAatsAsh ; cor=0.758; Ncor=0.758; logoDP=5.275; NIcor=0.702; NsEucl=0.941; SSD=3.022; NSW=0.928; rcor=23; rNcor=12; rlogoDP=21; rNIcor=11; rNsEucl=18; rSSD=24; rNSW=18; rank_mean=18.143; match_rank=20 a 64 52 22 14 199 10 0 0 17 2 61 25 47 257 254 176 45 16 189 63 69 c 68 73 29 137 17 8 4 46 241 132 7 2 3 2 1 15 47 105 23 77 68 g 57 72 22 102 24 12 1 4 1 4 143 226 200 0 3 56 41 129 23 72 57 t 71 63 187 7 20 230 255 210 1 122 49 7 10 1 2 13 127 10 25 48 66

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
local_words_7nt_m2_shift0 (local_words_7nt_m2)																	; local_words_7nt_m2; m=0 (reference); ncol1=21; shift=0; ncol=21; awaCATTTcybgkaaATGtaw ; Alignment reference a 36 33 74 5 114 3 2 4 15 15 17 19 18 83 81 91 9 4 30 39 34 c 28 23 15 105 4 2 1 2 70 62 41 21 3 10 11 7 4 6 16 28 24 g 30 26 14 8 3 3 0 0 10 5 34 69 50 21 19 5 2 111 10 27 25 t 31 43 22 7 4 117 122 119 30 43 33 16 54 11 14 22 110 4 69 31 42
local_words_7nt_m3_shift0 (local_words_7nt_m3)	0.942	0.942	5.912	0.929	0.972	0.693	0.983	8	3	14	4	3	8	5	6.429	6	; local_words_7nt_m2 versus local_words_7nt_m3; m=1/2; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 6.4286; kdaCATTTyCmrgaAATGtmw ; cor=0.942; Ncor=0.942; logoDP=5.912; NIcor=0.929; NsEucl=0.972; SSD=0.693; NSW=0.983; rcor=8; rNcor=3; rlogoDP=14; rNIcor=4; rNsEucl=3; rSSD=8; rNSW=5; rank_mean=6.429; match_rank=6 a 38 43 81 8 142 9 3 13 24 22 40 68 25 103 157 154 13 10 36 48 40 c 26 35 15 136 4 5 3 5 85 112 75 13 7 11 0 3 9 11 17 40 36 g 43 41 27 6 6 8 0 10 8 0 10 65 96 34 2 1 9 127 21 37 32 t 53 41 37 10 8 138 154 132 43 26 35 14 32 12 1 2 129 12 86 35 52
positions_7nt_m2_rc_shift0 (positions_7nt_m2_rc)	0.758	0.758	5.275	0.702	0.941	3.022	0.928	23	12	21	11	18	24	18	18.143	20	; local_words_7nt_m2 versus positions_7nt_m2_rc; m=2/2; ncol2=21; w=21; offset=0; strand=R; shift=0; score=18.1429; ysTsATTTCygGGAAatsAsh ; cor=0.758; Ncor=0.758; logoDP=5.275; NIcor=0.702; NsEucl=0.941; SSD=3.022; NSW=0.928; rcor=23; rNcor=12; rlogoDP=21; rNIcor=11; rNsEucl=18; rSSD=24; rNSW=18; rank_mean=18.143; match_rank=20 a 64 52 22 14 199 10 0 0 17 2 61 25 47 257 254 176 45 16 189 63 69 c 68 73 29 137 17 8 4 46 241 132 7 2 3 2 1 15 47 105 23 77 68 g 57 72 22 102 24 12 1 4 1 4 143 226 200 0 3 56 41 129 23 72 57 t 71 63 187 7 20 230 255 210 1 122 49 7 10 1 2 13 127 10 25 48 66

One-to-n matrix alignment; reference matrix: local_words_7nt_m3_shift0 ; 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
local_words_7nt_m3_shift0 (local_words_7nt_m3)
; local_words_7nt_m3; m=0 (reference); ncol1=21; shift=0; ncol=21; kdaCATTTyCmrgaAATGtmw ; Alignment reference a 38 43 81 8 142 9 3 13 24 22 40 68 25 103 157 154 13 10 36 48 40 c 26 35 15 136 4 5 3 5 85 112 75 13 7 11 0 3 9 11 17 40 36 g 43 41 27 6 6 8 0 10 8 0 10 65 96 34 2 1 9 127 21 37 32 t 53 41 37 10 8 138 154 132 43 26 35 14 32 12 1 2 129 12 86 35 52

positions_7nt_m2_shift0 (positions_7nt_m2) 0.842 0.842 6.437 0.812 0.952 2.019 0.952 14 7 10 7 11 14 14 11.000 8
; local_words_7nt_m3 versus positions_7nt_m2; m=1/5; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 11; dsTsatTTCCcrGAAATsAsr ; cor=0.842; Ncor=0.842; logoDP=6.437; NIcor=0.812; NsEucl=0.952; SSD=2.019; NSW=0.952; rcor=14; rNcor=7; rlogoDP=10; rNIcor=7; rNsEucl=11; rSSD=14; rNSW=14; rank_mean=11.000; match_rank=8 a 66 48 25 10 127 13 2 1 10 7 49 122 1 210 255 230 20 7 187 63 71 c 57 72 23 129 41 56 3 0 200 226 143 4 1 4 1 12 24 102 22 72 57 g 68 77 23 105 47 15 1 2 3 2 7 132 241 46 4 8 17 137 29 73 68 t 69 63 189 16 45 176 254 257 47 25 61 2 17 0 0 10 199 14 22 52 64

positions_7nt_m1_rc_shift0 (positions_7nt_m1_rc) 0.774 0.774 5.740 0.734 0.943 2.822 0.933 21 11 17 10 17 23 17 16.571 17
; local_words_7nt_m3 versus positions_7nt_m1_rc; m=2/5; ncol2=21; w=21; offset=0; strand=R; shift=0; score=16.5714; tsTsatTTCCwGGAAAysAsw ; cor=0.774; Ncor=0.774; logoDP=5.740; NIcor=0.734; NsEucl=0.943; SSD=2.822; NSW=0.933; rcor=21; rNcor=11; rlogoDP=17; rNIcor=10; rNsEucl=17; rSSD=23; rNSW=17; rank_mean=16.571; match_rank=17 a 116 96 46 27 289 62 2 2 47 7 142 28 4 446 479 334 27 35 340 91 131 c 113 131 51 244 23 105 2 2 400 395 97 3 2 6 2 19 137 247 53 148 112 g 117 143 57 196 87 30 3 8 4 2 92 442 401 28 2 113 31 167 39 138 117 t 138 114 330 17 85 287 477 472 33 80 153 11 77 4 1 18 289 35 52 107 124

oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1) 0.785 0.524 5.874 0.471 0.922 2.400 0.914 20 22 15 18 22 20 22 19.857 21
; local_words_7nt_m3 versus oligos_7nt_mkv4_m1; m=3/5; ncol2=14; w=14; offset=3; strand=D; shift=3; score=19.8571; ---srTTTCCwGGAAay---- ; cor=0.785; Ncor=0.524; logoDP=5.874; NIcor=0.471; NsEucl=0.922; SSD=2.400; NSW=0.914; rcor=20; rNcor=22; rlogoDP=15; rNIcor=18; rNsEucl=22; rSSD=20; rNSW=22; rank_mean=19.857; match_rank=21 a 0 0 0 237 426 84 1 1 178 0 456 265 0 1319 1318 550 257 0 0 0 0 c 0 0 0 455 268 57 1 40 1142 1320 266 1 0 0 2 202 358 0 0 0 0 g 0 0 0 349 370 74 0 0 0 0 176 1054 1138 0 0 315 228 0 0 0 0 t 0 0 0 279 256 1105 1318 1279 0 0 422 0 182 1 0 253 477 0 0 0 0

positions_7nt_m3_rc_shift2 (positions_7nt_m3_rc) 0.797 0.607 3.470 0.166 0.932 2.394 0.925 19 17 24 24 20 19 20 20.429 22
; local_words_7nt_m3 versus positions_7nt_m3_rc; m=4/5; ncol2=16; w=16; offset=2; strand=R; shift=2; score=20.4286; --ysayTTCCwRGAAAys--- ; cor=0.797; Ncor=0.607; logoDP=3.470; NIcor=0.166; NsEucl=0.932; SSD=2.394; NSW=0.925; rcor=19; rNcor=17; rlogoDP=24; rNIcor=24; rNsEucl=20; rSSD=19; rNSW=20; rank_mean=20.429; match_rank=22 a 0 0 237 218 723 148 4 3 39 4 398 343 4 1229 1223 894 229 265 0 0 0 c 0 0 317 453 156 411 2 1 1157 1196 306 1 3 2 7 66 329 375 0 0 0 g 0 0 279 326 216 44 3 2 2 7 153 892 1125 3 4 86 246 372 0 0 0 t 0 0 404 240 142 634 1228 1231 39 30 380 1 105 3 3 191 433 225 0 0 0

oligos_7nt_mkv4_m3_shift4 (oligos_7nt_mkv4_m3) 0.770 0.477 5.615 0.420 0.914 2.484 0.904 22 23 18 19 23 21 23 21.286 23
; local_words_7nt_m3 versus oligos_7nt_mkv4_m3; m=5/5; ncol2=13; w=13; offset=4; strand=D; shift=4; score=21.2857; ----ryTTCCmrGAAry---- ; cor=0.770; Ncor=0.477; logoDP=5.615; NIcor=0.420; NsEucl=0.914; SSD=2.484; NSW=0.904; rcor=22; rNcor=23; rlogoDP=18; rNIcor=19; rNsEucl=23; rSSD=21; rNSW=23; rank_mean=21.286; match_rank=23 a 0 0 0 0 381 217 0 4 8 1 597 450 1 1213 1217 492 233 0 0 0 0 c 0 0 0 0 271 347 0 0 1168 1214 612 1 0 3 2 185 354 0 0 0 0 g 0 0 0 0 337 158 3 1 0 4 10 768 1195 0 0 333 244 0 0 0 0 t 0 0 0 0 230 497 1216 1214 43 0 0 0 23 3 0 209 388 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
local_words_7nt_m3_shift0 (local_words_7nt_m3)																	; local_words_7nt_m3; m=0 (reference); ncol1=21; shift=0; ncol=21; kdaCATTTyCmrgaAATGtmw ; Alignment reference a 38 43 81 8 142 9 3 13 24 22 40 68 25 103 157 154 13 10 36 48 40 c 26 35 15 136 4 5 3 5 85 112 75 13 7 11 0 3 9 11 17 40 36 g 43 41 27 6 6 8 0 10 8 0 10 65 96 34 2 1 9 127 21 37 32 t 53 41 37 10 8 138 154 132 43 26 35 14 32 12 1 2 129 12 86 35 52
positions_7nt_m2_shift0 (positions_7nt_m2)	0.842	0.842	6.437	0.812	0.952	2.019	0.952	14	7	10	7	11	14	14	11.000	8	; local_words_7nt_m3 versus positions_7nt_m2; m=1/5; ncol2=21; w=21; offset=0; strand=D; shift=0; score= 11; dsTsatTTCCcrGAAATsAsr ; cor=0.842; Ncor=0.842; logoDP=6.437; NIcor=0.812; NsEucl=0.952; SSD=2.019; NSW=0.952; rcor=14; rNcor=7; rlogoDP=10; rNIcor=7; rNsEucl=11; rSSD=14; rNSW=14; rank_mean=11.000; match_rank=8 a 66 48 25 10 127 13 2 1 10 7 49 122 1 210 255 230 20 7 187 63 71 c 57 72 23 129 41 56 3 0 200 226 143 4 1 4 1 12 24 102 22 72 57 g 68 77 23 105 47 15 1 2 3 2 7 132 241 46 4 8 17 137 29 73 68 t 69 63 189 16 45 176 254 257 47 25 61 2 17 0 0 10 199 14 22 52 64
positions_7nt_m1_rc_shift0 (positions_7nt_m1_rc)	0.774	0.774	5.740	0.734	0.943	2.822	0.933	21	11	17	10	17	23	17	16.571	17	; local_words_7nt_m3 versus positions_7nt_m1_rc; m=2/5; ncol2=21; w=21; offset=0; strand=R; shift=0; score=16.5714; tsTsatTTCCwGGAAAysAsw ; cor=0.774; Ncor=0.774; logoDP=5.740; NIcor=0.734; NsEucl=0.943; SSD=2.822; NSW=0.933; rcor=21; rNcor=11; rlogoDP=17; rNIcor=10; rNsEucl=17; rSSD=23; rNSW=17; rank_mean=16.571; match_rank=17 a 116 96 46 27 289 62 2 2 47 7 142 28 4 446 479 334 27 35 340 91 131 c 113 131 51 244 23 105 2 2 400 395 97 3 2 6 2 19 137 247 53 148 112 g 117 143 57 196 87 30 3 8 4 2 92 442 401 28 2 113 31 167 39 138 117 t 138 114 330 17 85 287 477 472 33 80 153 11 77 4 1 18 289 35 52 107 124
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)	0.785	0.524	5.874	0.471	0.922	2.400	0.914	20	22	15	18	22	20	22	19.857	21	; local_words_7nt_m3 versus oligos_7nt_mkv4_m1; m=3/5; ncol2=14; w=14; offset=3; strand=D; shift=3; score=19.8571; ---srTTTCCwGGAAay---- ; cor=0.785; Ncor=0.524; logoDP=5.874; NIcor=0.471; NsEucl=0.922; SSD=2.400; NSW=0.914; rcor=20; rNcor=22; rlogoDP=15; rNIcor=18; rNsEucl=22; rSSD=20; rNSW=22; rank_mean=19.857; match_rank=21 a 0 0 0 237 426 84 1 1 178 0 456 265 0 1319 1318 550 257 0 0 0 0 c 0 0 0 455 268 57 1 40 1142 1320 266 1 0 0 2 202 358 0 0 0 0 g 0 0 0 349 370 74 0 0 0 0 176 1054 1138 0 0 315 228 0 0 0 0 t 0 0 0 279 256 1105 1318 1279 0 0 422 0 182 1 0 253 477 0 0 0 0
positions_7nt_m3_rc_shift2 (positions_7nt_m3_rc)	0.797	0.607	3.470	0.166	0.932	2.394	0.925	19	17	24	24	20	19	20	20.429	22	; local_words_7nt_m3 versus positions_7nt_m3_rc; m=4/5; ncol2=16; w=16; offset=2; strand=R; shift=2; score=20.4286; --ysayTTCCwRGAAAys--- ; cor=0.797; Ncor=0.607; logoDP=3.470; NIcor=0.166; NsEucl=0.932; SSD=2.394; NSW=0.925; rcor=19; rNcor=17; rlogoDP=24; rNIcor=24; rNsEucl=20; rSSD=19; rNSW=20; rank_mean=20.429; match_rank=22 a 0 0 237 218 723 148 4 3 39 4 398 343 4 1229 1223 894 229 265 0 0 0 c 0 0 317 453 156 411 2 1 1157 1196 306 1 3 2 7 66 329 375 0 0 0 g 0 0 279 326 216 44 3 2 2 7 153 892 1125 3 4 86 246 372 0 0 0 t 0 0 404 240 142 634 1228 1231 39 30 380 1 105 3 3 191 433 225 0 0 0
oligos_7nt_mkv4_m3_shift4 (oligos_7nt_mkv4_m3)	0.770	0.477	5.615	0.420	0.914	2.484	0.904	22	23	18	19	23	21	23	21.286	23	; local_words_7nt_m3 versus oligos_7nt_mkv4_m3; m=5/5; ncol2=13; w=13; offset=4; strand=D; shift=4; score=21.2857; ----ryTTCCmrGAAry---- ; cor=0.770; Ncor=0.477; logoDP=5.615; NIcor=0.420; NsEucl=0.914; SSD=2.484; NSW=0.904; rcor=22; rNcor=23; rlogoDP=18; rNIcor=19; rNsEucl=23; rSSD=21; rNSW=23; rank_mean=21.286; match_rank=23 a 0 0 0 0 381 217 0 4 8 1 597 450 1 1213 1217 492 233 0 0 0 0 c 0 0 0 0 271 347 0 0 1168 1214 612 1 0 3 2 185 354 0 0 0 0 g 0 0 0 0 337 158 3 1 0 4 10 768 1195 0 0 333 244 0 0 0 0 t 0 0 0 0 230 497 1216 1214 43 0 0 0 23 3 0 209 388 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift4 ; 4 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_7nt_mkv4_m3_shift4 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=13; shift=4; ncol=21; ----ryTTCCmrGAAry---- ; Alignment reference a 0 0 0 0 381 217 0 4 8 1 597 450 1 1213 1217 492 233 0 0 0 0 c 0 0 0 0 271 347 0 0 1168 1214 612 1 0 3 2 185 354 0 0 0 0 g 0 0 0 0 337 158 3 1 0 4 10 768 1195 0 0 333 244 0 0 0 0 t 0 0 0 0 230 497 1216 1214 43 0 0 0 23 3 0 209 388 0 0 0 0

positions_7nt_m1_shift0 (positions_7nt_m1) 0.927 0.574 9.770 0.577 0.951 0.819 0.968 10 19 3 14 12 10 10 11.143 9
; oligos_7nt_mkv4_m3 versus positions_7nt_m1; m=1/3; ncol2=21; w=13; offset=-4; strand=D; shift=0; score=11.1429; wsTsrTTTCCwGGAAatsAsa ; cor=0.927; Ncor=0.574; logoDP=9.770; NIcor=0.577; NsEucl=0.951; SSD=0.819; NSW=0.968; rcor=10; rNcor=19; rlogoDP=3; rNIcor=14; rNsEucl=12; rSSD=10; rNSW=10; rank_mean=11.143; match_rank=9 a 124 107 52 35 289 18 1 4 77 11 153 80 33 472 477 287 85 17 330 114 138 c 117 138 39 167 31 113 2 28 401 442 92 2 4 8 3 30 87 196 57 143 117 g 112 148 53 247 137 19 2 6 2 3 97 395 400 2 2 105 23 244 51 131 113 t 131 91 340 35 27 334 479 446 4 28 142 7 47 2 2 62 289 27 46 96 116

positions_7nt_m3_rc_shift2 (positions_7nt_m3_rc) 0.956 0.777 5.037 0.262 0.961 0.509 0.980 5 10 22 22 8 5 7 11.286 10
; oligos_7nt_mkv4_m3 versus positions_7nt_m3_rc; m=2/3; ncol2=16; w=13; offset=-2; strand=R; shift=2; score=11.2857; --ysayTTCCwRGAAAys--- ; cor=0.956; Ncor=0.777; logoDP=5.037; NIcor=0.262; NsEucl=0.961; SSD=0.509; NSW=0.980; rcor=5; rNcor=10; rlogoDP=22; rNIcor=22; rNsEucl=8; rSSD=5; rNSW=7; rank_mean=11.286; match_rank=10 a 0 0 237 218 723 148 4 3 39 4 398 343 4 1229 1223 894 229 265 0 0 0 c 0 0 317 453 156 411 2 1 1157 1196 306 1 3 2 7 66 329 375 0 0 0 g 0 0 279 326 216 44 3 2 2 7 153 892 1125 3 4 86 246 372 0 0 0 t 0 0 404 240 142 634 1228 1231 39 30 380 1 105 3 3 191 433 225 0 0 0

positions_7nt_m2_shift0 (positions_7nt_m2) 0.907 0.561 9.364 0.549 0.944 1.063 0.959 12 20 5 16 16 11 12 13.143 14
; oligos_7nt_mkv4_m3 versus positions_7nt_m2; m=3/3; ncol2=21; w=13; offset=-4; strand=D; shift=0; score=13.1429; dsTsatTTCCcrGAAATsAsr ; cor=0.907; Ncor=0.561; logoDP=9.364; NIcor=0.549; NsEucl=0.944; SSD=1.063; NSW=0.959; rcor=12; rNcor=20; rlogoDP=5; rNIcor=16; rNsEucl=16; rSSD=11; rNSW=12; rank_mean=13.143; match_rank=14 a 66 48 25 10 127 13 2 1 10 7 49 122 1 210 255 230 20 7 187 63 71 c 57 72 23 129 41 56 3 0 200 226 143 4 1 4 1 12 24 102 22 72 57 g 68 77 23 105 47 15 1 2 3 2 7 132 241 46 4 8 17 137 29 73 68 t 69 63 189 16 45 176 254 257 47 25 61 2 17 0 0 10 199 14 22 52 64

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv4_m3_shift4 (oligos_7nt_mkv4_m3)																	; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=13; shift=4; ncol=21; ----ryTTCCmrGAAry---- ; Alignment reference a 0 0 0 0 381 217 0 4 8 1 597 450 1 1213 1217 492 233 0 0 0 0 c 0 0 0 0 271 347 0 0 1168 1214 612 1 0 3 2 185 354 0 0 0 0 g 0 0 0 0 337 158 3 1 0 4 10 768 1195 0 0 333 244 0 0 0 0 t 0 0 0 0 230 497 1216 1214 43 0 0 0 23 3 0 209 388 0 0 0 0
positions_7nt_m1_shift0 (positions_7nt_m1)	0.927	0.574	9.770	0.577	0.951	0.819	0.968	10	19	3	14	12	10	10	11.143	9	; oligos_7nt_mkv4_m3 versus positions_7nt_m1; m=1/3; ncol2=21; w=13; offset=-4; strand=D; shift=0; score=11.1429; wsTsrTTTCCwGGAAatsAsa ; cor=0.927; Ncor=0.574; logoDP=9.770; NIcor=0.577; NsEucl=0.951; SSD=0.819; NSW=0.968; rcor=10; rNcor=19; rlogoDP=3; rNIcor=14; rNsEucl=12; rSSD=10; rNSW=10; rank_mean=11.143; match_rank=9 a 124 107 52 35 289 18 1 4 77 11 153 80 33 472 477 287 85 17 330 114 138 c 117 138 39 167 31 113 2 28 401 442 92 2 4 8 3 30 87 196 57 143 117 g 112 148 53 247 137 19 2 6 2 3 97 395 400 2 2 105 23 244 51 131 113 t 131 91 340 35 27 334 479 446 4 28 142 7 47 2 2 62 289 27 46 96 116
positions_7nt_m3_rc_shift2 (positions_7nt_m3_rc)	0.956	0.777	5.037	0.262	0.961	0.509	0.980	5	10	22	22	8	5	7	11.286	10	; oligos_7nt_mkv4_m3 versus positions_7nt_m3_rc; m=2/3; ncol2=16; w=13; offset=-2; strand=R; shift=2; score=11.2857; --ysayTTCCwRGAAAys--- ; cor=0.956; Ncor=0.777; logoDP=5.037; NIcor=0.262; NsEucl=0.961; SSD=0.509; NSW=0.980; rcor=5; rNcor=10; rlogoDP=22; rNIcor=22; rNsEucl=8; rSSD=5; rNSW=7; rank_mean=11.286; match_rank=10 a 0 0 237 218 723 148 4 3 39 4 398 343 4 1229 1223 894 229 265 0 0 0 c 0 0 317 453 156 411 2 1 1157 1196 306 1 3 2 7 66 329 375 0 0 0 g 0 0 279 326 216 44 3 2 2 7 153 892 1125 3 4 86 246 372 0 0 0 t 0 0 404 240 142 634 1228 1231 39 30 380 1 105 3 3 191 433 225 0 0 0
positions_7nt_m2_shift0 (positions_7nt_m2)	0.907	0.561	9.364	0.549	0.944	1.063	0.959	12	20	5	16	16	11	12	13.143	14	; oligos_7nt_mkv4_m3 versus positions_7nt_m2; m=3/3; ncol2=21; w=13; offset=-4; strand=D; shift=0; score=13.1429; dsTsatTTCCcrGAAATsAsr ; cor=0.907; Ncor=0.561; logoDP=9.364; NIcor=0.549; NsEucl=0.944; SSD=1.063; NSW=0.959; rcor=12; rNcor=20; rlogoDP=5; rNIcor=16; rNsEucl=16; rSSD=11; rNSW=12; rank_mean=13.143; match_rank=14 a 66 48 25 10 127 13 2 1 10 7 49 122 1 210 255 230 20 7 187 63 71 c 57 72 23 129 41 56 3 0 200 226 143 4 1 4 1 12 24 102 22 72 57 g 68 77 23 105 47 15 1 2 3 2 7 132 241 46 4 8 17 137 29 73 68 t 69 63 189 16 45 176 254 257 47 25 61 2 17 0 0 10 199 14 22 52 64

One-to-n matrix alignment; reference matrix: positions_7nt_m2_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_m2_shift0 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=21; shift=0; ncol=21; dsTsatTTCCcrGAAATsAsr ; Alignment reference a 66 48 25 10 127 13 2 1 10 7 49 122 1 210 255 230 20 7 187 63 71 c 57 72 23 129 41 56 3 0 200 226 143 4 1 4 1 12 24 102 22 72 57 g 68 77 23 105 47 15 1 2 3 2 7 132 241 46 4 8 17 137 29 73 68 t 69 63 189 16 45 176 254 257 47 25 61 2 17 0 0 10 199 14 22 52 64

positions_7nt_m3_rc_shift2 (positions_7nt_m3_rc) 0.913 0.696 3.888 0.201 0.954 1.072 0.967 11 14 23 23 10 12 11 14.857 16
; positions_7nt_m2 versus positions_7nt_m3_rc; m=1/1; ncol2=16; w=16; offset=2; strand=R; shift=2; score=14.8571; --ysayTTCCwRGAAAys--- ; cor=0.913; Ncor=0.696; logoDP=3.888; NIcor=0.201; NsEucl=0.954; SSD=1.072; NSW=0.967; rcor=11; rNcor=14; rlogoDP=23; rNIcor=23; rNsEucl=10; rSSD=12; rNSW=11; rank_mean=14.857; match_rank=16 a 0 0 237 218 723 148 4 3 39 4 398 343 4 1229 1223 894 229 265 0 0 0 c 0 0 317 453 156 411 2 1 1157 1196 306 1 3 2 7 66 329 375 0 0 0 g 0 0 279 326 216 44 3 2 2 7 153 892 1125 3 4 86 246 372 0 0 0 t 0 0 404 240 142 634 1228 1231 39 30 380 1 105 3 3 191 433 225 0 0 0