One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 9 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor 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=18; shift=0; ncol=19; aakgATTGTGCAATcawt-
; Alignment reference
a	18	18	9	6	48	1	0	3	2	0	4	54	55	3	6	36	14	13	0
c	13	13	7	6	2	0	0	0	3	0	51	0	0	3	36	9	12	9	0
g	12	13	14	30	4	0	0	52	2	55	0	0	0	1	5	6	11	13	0
t	12	11	25	13	1	54	55	0	48	0	0	1	0	48	8	4	18	20	0
positions_7nt_m1_shift1 (positions_7nt_m1) 0.992 0.937 13.192 0.939 0.986 0.111 0.997 1 2 2 3 1 1 1 1.571 1 
; positions_6nt_m1 versus positions_7nt_m1; m=1/8; ncol2=17; w=17; offset=1; strand=D; shift=1; score= 1.5714; -rdgATTGTGCAATcAtt-
; cor=0.992; Ncor=0.937; logoDP=13.192; NIcor=0.939; NsEucl=0.986; SSD=0.111; NSW=0.997; rcor=1; rNcor=2; rlogoDP=2; rNIcor=3; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.571; match_rank=1
a	0	23	21	11	66	0	0	3	3	0	6	74	75	5	7	52	17	18	0
c	0	17	11	10	1	0	0	0	4	0	69	0	0	8	48	10	18	17	0
g	0	22	24	43	6	0	0	71	2	75	0	0	0	5	11	6	17	16	0
t	0	13	19	11	2	75	75	1	66	0	0	1	0	57	9	7	23	24	0
positions_6nt_m3_shift0 (positions_6nt_m3) 0.955 0.955 12.977 0.963 0.968 0.645 0.982 11 1 4 1 8 12 10 6.714 3 
; positions_6nt_m1 versus positions_6nt_m3; m=2/8; ncol2=18; w=18; offset=0; strand=D; shift=0; score= 6.7143; catgATTGTGCAATartt-
; cor=0.955; Ncor=0.955; logoDP=12.977; NIcor=0.963; NsEucl=0.968; SSD=0.645; NSW=0.982; rcor=11; rNcor=1; rlogoDP=4; rNIcor=1; rNsEucl=8; rSSD=12; rNSW=10; rank_mean=6.714; match_rank=3
a	12	17	7	4	46	0	0	1	1	0	4	51	53	0	29	25	12	13	0
c	16	12	5	7	3	0	0	0	4	0	45	0	0	2	6	5	12	9	0
g	13	13	9	31	2	0	0	51	0	53	1	1	0	5	9	14	12	11	0
t	12	11	32	11	2	53	53	1	48	0	3	1	0	46	9	9	17	20	0
positions_6nt_m4_shift0 (positions_6nt_m4) 0.908 0.908 11.706 0.904 0.956 1.281 0.964 26 6 21 5 18 29 20 17.857 12 
; positions_6nt_m1 versus positions_6nt_m4; m=3/8; ncol2=18; w=18; offset=0; strand=D; shift=0; score=17.8571; mbtgATTGCGCAATcavk-
; cor=0.908; Ncor=0.908; logoDP=11.706; NIcor=0.904; NsEucl=0.956; SSD=1.281; NSW=0.964; rcor=26; rNcor=6; rlogoDP=21; rNIcor=5; rNsEucl=18; rSSD=29; rNSW=20; rank_mean=17.857; match_rank=12
a	14	9	6	4	40	0	0	0	3	6	3	46	46	1	5	24	12	9	0
c	13	13	7	6	3	0	0	0	35	2	43	0	0	2	31	9	12	10	0
g	10	12	9	31	2	0	0	43	2	35	0	0	0	3	6	7	13	13	0
t	9	12	24	5	1	46	46	3	6	3	0	0	0	40	4	6	9	14	0
positions_7nt_m2_shift0 (positions_7nt_m2) 0.867 0.867 10.942 0.869 0.947 1.796 0.950 53 15 30 11 29 56 34 32.571 24 
; positions_6nt_m1 versus positions_7nt_m2; m=4/8; ncol2=18; w=18; offset=0; strand=D; shift=0; score=32.5714; ayttATTGCGCAATaarw-
; cor=0.867; Ncor=0.867; logoDP=10.942; NIcor=0.869; NsEucl=0.947; SSD=1.796; NSW=0.950; rcor=53; rNcor=15; rlogoDP=30; rNIcor=11; rNsEucl=29; rSSD=56; rNSW=34; rank_mean=32.571; match_rank=24
a	35	28	19	17	94	0	1	3	4	19	5	113	114	5	56	51	29	29	0
c	27	33	27	18	10	1	0	0	90	2	107	1	0	6	23	18	26	25	0
g	25	25	18	23	6	0	1	108	2	90	0	0	1	10	19	27	32	26	0
t	28	29	51	57	5	114	113	4	19	4	3	1	0	94	17	19	28	35	0
positions_6nt_m5_rc_shift2 (positions_6nt_m5_rc) 0.913 0.812 5.511 0.220 0.951 1.218 0.962 22 28 78 82 25 25 24 40.571 34 
; positions_6nt_m1 versus positions_6nt_m5_rc; m=5/8; ncol2=16; w=16; offset=2; strand=R; shift=2; score=40.5714; --rtGTTGTGCAATcamt-
; cor=0.913; Ncor=0.812; logoDP=5.511; NIcor=0.220; NsEucl=0.951; SSD=1.218; NSW=0.962; rcor=22; rNcor=28; rlogoDP=78; rNIcor=82; rNsEucl=25; rSSD=25; rNSW=24; rank_mean=40.571; match_rank=34
a	0	0	26	19	16	0	0	5	0	0	2	79	79	1	10	45	22	17	0
c	0	0	11	13	5	0	0	0	4	0	74	0	0	7	48	9	23	16	0
g	0	0	28	17	57	0	0	74	1	79	1	0	0	2	10	7	19	15	0
t	0	0	14	30	1	79	79	0	74	0	2	0	0	69	11	18	15	31	0
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc) 0.905 0.855 4.211 0.075 0.952 1.346 0.960 27 20 87 90 24 34 26 44.000 43 
; positions_6nt_m1 versus positions_7nt_m4_rc; m=6/8; ncol2=17; w=17; offset=1; strand=R; shift=1; score=     44; -rraGTTGTGCAATcAry-
; cor=0.905; Ncor=0.855; logoDP=4.211; NIcor=0.075; NsEucl=0.952; SSD=1.346; NSW=0.960; rcor=27; rNcor=20; rlogoDP=87; rNIcor=90; rNsEucl=24; rSSD=34; rNSW=26; rank_mean=44.000; match_rank=43
a	0	25	23	36	17	0	0	3	3	0	3	72	72	3	9	51	19	13	0
c	0	13	13	9	2	0	0	0	3	0	68	0	0	10	44	7	15	18	0
g	0	19	24	10	52	0	1	69	2	72	1	0	0	1	9	5	23	11	0
t	0	15	12	17	1	72	71	0	64	0	0	0	0	58	10	9	15	30	0
positions_7nt_m5_shift1 (positions_7nt_m5) 0.827 0.740 12.941 0.753 0.934 2.484 0.927 74 48 5 28 54 77 66 50.286 49 
; positions_6nt_m1 versus positions_7nt_m5; m=7/8; ncol2=18; w=17; offset=1; strand=D; shift=1; score=50.2857; -gwgATTGTGCAACAchkr
; cor=0.827; Ncor=0.740; logoDP=12.941; NIcor=0.753; NsEucl=0.934; SSD=2.484; NSW=0.927; rcor=74; rNcor=48; rlogoDP=5; rNIcor=28; rNsEucl=54; rSSD=77; rNSW=66; rank_mean=50.286; match_rank=49
a	0	11	18	8	49	0	0	1	3	0	1	53	54	2	42	5	22	12	18
c	0	13	7	12	3	0	0	0	3	0	50	1	0	41	7	29	15	6	11
g	0	21	10	29	1	0	0	53	2	54	1	0	0	5	2	10	3	17	15
t	0	9	19	5	1	54	54	0	46	0	2	0	0	6	3	10	14	19	10
positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc) 0.823 0.823 10.349 0.644 0.937 2.581 0.928 75 25 42 43 49 82 64 54.286 56 
; positions_6nt_m1 versus positions_6nt_m2_rc; m=8/8; ncol2=18; w=18; offset=0; strand=R; shift=0; score=54.2857; wgtgATTGTGCAACAcwk-
; cor=0.823; Ncor=0.823; logoDP=10.349; NIcor=0.644; NsEucl=0.937; SSD=2.581; NSW=0.928; rcor=75; rNcor=25; rlogoDP=42; rNIcor=43; rNsEucl=49; rSSD=82; rNSW=64; rank_mean=54.286; match_rank=56
a	12	8	7	4	38	0	1	1	1	0	1	42	42	2	31	2	20	9	0
c	7	9	3	9	3	1	0	0	3	0	39	0	0	31	5	27	8	7	0
g	8	16	6	24	1	0	0	40	1	42	0	0	0	4	2	7	1	14	0
t	15	9	26	5	0	41	41	1	37	0	2	0	0	5	4	6	13	12	0

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift1 ; 5 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_m5_shift1 (positions_6nt_m5)                                 
; positions_6nt_m5; m=0 (reference); ncol1=16; shift=1; ncol=18; -aktgATTGCACAACay-
; Alignment reference
a	0	31	15	18	11	69	0	0	2	0	74	0	79	79	1	30	14	0
c	0	15	19	7	10	2	0	0	1	79	1	74	0	0	57	17	28	0
g	0	16	23	9	48	7	0	0	74	0	4	0	0	0	5	13	11	0
t	0	17	22	45	10	1	79	79	2	0	0	5	0	0	16	19	26	0
positions_7nt_m4_shift1 (positions_7nt_m4) 0.988 0.930 13.492 0.931 0.982 0.164 0.995 3 4 1 4 3 3 3 3.000 2 
; positions_6nt_m5 versus positions_7nt_m4; m=1/4; ncol2=17; w=16; offset=0; strand=D; shift=1; score=      3; -ryTgATTGCACAACtyy
; cor=0.988; Ncor=0.930; logoDP=13.492; NIcor=0.931; NsEucl=0.982; SSD=0.164; NSW=0.995; rcor=3; rNcor=4; rlogoDP=1; rNIcor=4; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.000; match_rank=2
a	0	30	15	9	10	58	0	0	0	0	64	0	71	72	1	17	12	15
c	0	11	23	5	9	1	0	0	1	72	2	69	1	0	52	10	24	19
g	0	18	15	7	44	10	0	0	68	0	3	0	0	0	2	9	13	13
t	0	13	19	51	9	3	72	72	3	0	3	3	0	0	17	36	23	25
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc) 0.916 0.862 4.258 0.084 0.952 1.166 0.964 21 17 86 87 22 23 23 39.857 32 
; positions_6nt_m5 versus positions_7nt_m1_rc; m=2/4; ncol2=17; w=16; offset=0; strand=R; shift=1; score=39.8571; -aaTgATTGCACAATchy
; cor=0.916; Ncor=0.862; logoDP=4.258; NIcor=0.084; NsEucl=0.952; SSD=1.166; NSW=0.964; rcor=21; rNcor=17; rlogoDP=86; rNIcor=87; rNsEucl=22; rSSD=23; rNSW=23; rank_mean=39.857; match_rank=32
a	0	24	23	7	9	57	0	1	0	0	66	1	75	75	2	11	19	13
c	0	16	17	6	11	5	0	0	0	75	2	71	0	0	6	43	24	22
g	0	17	18	10	48	8	0	0	69	0	4	0	0	0	1	10	11	17
t	0	18	17	52	7	5	75	74	6	0	3	3	0	0	66	11	21	23
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc) 0.803 0.713 10.841 0.709 0.929 2.578 0.919 79 56 34 36 64 80 75 60.571 65 
; positions_6nt_m5 versus positions_7nt_m2_rc; m=3/4; ncol2=18; w=16; offset=0; strand=R; shift=1; score=60.5714; -wyttATTGCGCAATaar
; cor=0.803; Ncor=0.713; logoDP=10.841; NIcor=0.709; NsEucl=0.929; SSD=2.578; NSW=0.919; rcor=79; rNcor=56; rlogoDP=34; rNIcor=36; rNsEucl=64; rSSD=80; rNSW=75; rank_mean=60.571; match_rank=65
a	0	35	28	19	17	94	0	1	3	4	19	4	113	114	5	57	51	29
c	0	26	32	27	19	10	1	0	0	90	2	108	1	0	6	23	18	25
g	0	25	26	18	23	6	0	1	107	2	90	0	0	1	10	18	27	33
t	0	29	29	51	56	5	114	113	5	19	4	3	1	0	94	17	19	28
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc) 0.754 0.670 5.941 0.326 0.918 3.467 0.892 95 70 75 77 83 97 94 84.429 95 
; positions_6nt_m5 versus positions_7nt_m5_rc; m=4/4; ncol2=18; w=16; offset=-1; strand=R; shift=0; score=84.4286; ymdgTGTTGCACAATcwc
; cor=0.754; Ncor=0.670; logoDP=5.941; NIcor=0.326; NsEucl=0.918; SSD=3.467; NSW=0.892; rcor=95; rNcor=70; rlogoDP=75; rNIcor=77; rNsEucl=83; rSSD=97; rNSW=94; rank_mean=84.429; match_rank=95
a	10	19	14	10	3	6	0	0	2	0	46	0	54	54	1	5	19	9
c	15	17	3	10	2	5	0	0	1	54	2	53	0	0	1	29	10	21
g	11	6	15	29	7	41	0	1	50	0	3	0	0	0	3	12	7	13
t	18	12	22	5	42	2	54	53	1	0	3	1	0	0	49	8	18	11

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift3 ; 13 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)                                 
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=14; shift=3; ncol=18; ---wrATTGCACAAcwy-
; Alignment reference
a	0	0	0	72	59	190	1	0	11	1	209	3	233	233	4	90	46	0
c	0	0	0	55	56	14	0	0	2	234	8	223	2	0	153	53	71	0
g	0	0	0	39	63	26	0	1	213	0	9	2	0	0	22	28	54	0
t	0	0	0	69	57	5	234	234	9	0	9	7	0	2	56	64	64	0
positions_6nt_m5_shift1 (positions_6nt_m5) 0.978 0.856 12.856 0.858 0.972 0.299 0.989 5 19 7 14 7 5 6 9.000 4 
; oligos_7nt_mkv4_m2 versus positions_6nt_m5; m=1/12; ncol2=16; w=14; offset=-2; strand=D; shift=1; score=      9; -aktgATTGCACAACay-
; cor=0.978; Ncor=0.856; logoDP=12.856; NIcor=0.858; NsEucl=0.972; SSD=0.299; NSW=0.989; rcor=5; rNcor=19; rlogoDP=7; rNIcor=14; rNsEucl=7; rSSD=5; rNSW=6; rank_mean=9.000; match_rank=4
a	0	31	15	18	11	69	0	0	2	0	74	0	79	79	1	30	14	0
c	0	15	19	7	10	2	0	0	1	79	1	74	0	0	57	17	28	0
g	0	16	23	9	48	7	0	0	74	0	4	0	0	0	5	13	11	0
t	0	17	22	45	10	1	79	79	2	0	0	5	0	0	16	19	26	0
positions_7nt_m4_shift1 (positions_7nt_m4) 0.963 0.793 12.602 0.794 0.964 0.498 0.982 8 34 10 22 11 8 9 14.571 10 
; oligos_7nt_mkv4_m2 versus positions_7nt_m4; m=2/12; ncol2=17; w=14; offset=-2; strand=D; shift=1; score=14.5714; -ryTgATTGCACAACtyy
; cor=0.963; Ncor=0.793; logoDP=12.602; NIcor=0.794; NsEucl=0.964; SSD=0.498; NSW=0.982; rcor=8; rNcor=34; rlogoDP=10; rNIcor=22; rNsEucl=11; rSSD=8; rNSW=9; rank_mean=14.571; match_rank=10
a	0	30	15	9	10	58	0	0	0	0	64	0	71	72	1	17	12	15
c	0	11	23	5	9	1	0	0	1	72	2	69	1	0	52	10	24	19
g	0	18	15	7	44	10	0	0	68	0	3	0	0	0	2	9	13	13
t	0	13	19	51	9	3	72	72	3	0	3	3	0	0	17	36	23	25
oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3) 0.887 0.769 9.935 0.766 0.937 1.330 0.949 36 41 50 25 48 32 40 38.857 30 
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m3; m=3/12; ncol2=14; w=13; offset=-1; strand=D; shift=2; score=38.8571; --rwkATTTCACAAym--
; cor=0.887; Ncor=0.769; logoDP=9.935; NIcor=0.766; NsEucl=0.937; SSD=1.330; NSW=0.949; rcor=36; rNcor=41; rlogoDP=50; rNIcor=25; rNsEucl=48; rSSD=32; rNSW=40; rank_mean=38.857; match_rank=30
a	0	0	62	57	19	194	1	5	23	0	176	9	201	195	25	70	0	0
c	0	0	40	46	26	4	0	1	5	210	12	190	4	1	64	58	0	0
g	0	0	69	41	101	10	2	9	33	0	15	2	0	8	32	39	0	0
t	0	0	39	66	64	2	207	195	149	0	7	9	5	6	89	43	0	0
oligos_7nt_mkv4_m4_shift4 (oligos_7nt_mkv4_m4) 0.876 0.751 11.206 0.759 0.929 1.458 0.939 44 44 26 26 65 40 54 42.714 39 
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m4; m=4/12; ncol2=12; w=12; offset=1; strand=D; shift=4; score=42.7143; ----krTTGCkCAAyw--
; cor=0.876; Ncor=0.751; logoDP=11.206; NIcor=0.759; NsEucl=0.929; SSD=1.458; NSW=0.939; rcor=44; rNcor=44; rlogoDP=26; rNIcor=26; rNsEucl=65; rSSD=40; rNSW=54; rank_mean=42.714; match_rank=39
a	0	0	0	0	34	80	0	2	1	0	10	4	168	170	11	61	0	0
c	0	0	0	0	33	28	0	4	0	172	3	165	0	1	53	30	0	0
g	0	0	0	0	44	49	0	0	170	0	58	0	3	1	29	32	0	0
t	0	0	0	0	61	15	172	166	1	0	101	3	1	0	79	49	0	0
positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc) 0.897 0.698 9.925 0.500 0.940 1.399 0.950 30 63 51 68 40 38 35 46.429 46 
; oligos_7nt_mkv4_m2 versus positions_6nt_m1_rc; m=5/12; ncol2=18; w=14; offset=-2; strand=R; shift=1; score=46.4286; -awtgATTGCACAATcmt
; cor=0.897; Ncor=0.698; logoDP=9.925; NIcor=0.500; NsEucl=0.940; SSD=1.399; NSW=0.950; rcor=30; rNcor=63; rlogoDP=51; rNIcor=68; rNsEucl=40; rSSD=38; rNSW=35; rank_mean=46.429; match_rank=46
a	0	20	18	4	8	48	0	1	0	0	48	0	55	54	1	13	25	11
c	0	13	11	6	5	1	0	0	0	55	2	52	0	0	4	30	14	13
g	0	9	12	9	36	3	0	0	51	0	3	0	0	0	2	6	7	13
t	0	13	14	36	6	3	55	54	4	0	2	3	0	1	48	6	9	18
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc) 0.895 0.696 9.606 0.505 0.940 1.401 0.950 31 65 57 67 41 39 36 48.000 48 
; oligos_7nt_mkv4_m2 versus positions_6nt_m3_rc; m=6/12; ncol2=18; w=14; offset=-2; strand=R; shift=1; score=     48; -aaytATTGCACAATcat
; cor=0.895; Ncor=0.696; logoDP=9.606; NIcor=0.505; NsEucl=0.940; SSD=1.401; NSW=0.950; rcor=31; rNcor=65; rlogoDP=57; rNIcor=67; rNsEucl=41; rSSD=39; rNSW=36; rank_mean=48.000; match_rank=48
a	0	20	17	9	9	46	0	1	3	0	48	1	53	53	2	11	32	11
c	0	11	12	14	9	5	0	1	1	53	0	51	0	0	2	31	9	13
g	0	9	12	5	6	2	0	0	45	0	4	0	0	0	3	7	5	12
t	0	13	12	25	29	0	53	51	4	0	1	1	0	0	46	4	7	17
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc) 0.898 0.739 4.082 0.069 0.941 1.374 0.951 29 49 91 91 39 36 32 52.429 52 
; oligos_7nt_mkv4_m2 versus positions_7nt_m1_rc; m=7/12; ncol2=17; w=14; offset=-2; strand=R; shift=1; score=52.4286; -aaTgATTGCACAATchy
; cor=0.898; Ncor=0.739; logoDP=4.082; NIcor=0.069; NsEucl=0.941; SSD=1.374; NSW=0.951; rcor=29; rNcor=49; rlogoDP=91; rNIcor=91; rNsEucl=39; rSSD=36; rNSW=32; rank_mean=52.429; match_rank=52
a	0	24	23	7	9	57	0	1	0	0	66	1	75	75	2	11	19	13
c	0	16	17	6	11	5	0	0	0	75	2	71	0	0	6	43	24	22
g	0	17	18	10	48	8	0	0	69	0	4	0	0	0	1	10	11	17
t	0	18	17	52	7	5	75	74	6	0	3	3	0	0	66	11	21	23
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc) 0.828 0.644 10.271 0.641 0.927 2.102 0.925 73 74 44 45 71 69 69 63.571 69 
; oligos_7nt_mkv4_m2 versus positions_7nt_m2_rc; m=8/12; ncol2=18; w=14; offset=-2; strand=R; shift=1; score=63.5714; -wyttATTGCGCAATaar
; cor=0.828; Ncor=0.644; logoDP=10.271; NIcor=0.641; NsEucl=0.927; SSD=2.102; NSW=0.925; rcor=73; rNcor=74; rlogoDP=44; rNIcor=45; rNsEucl=71; rSSD=69; rNSW=69; rank_mean=63.571; match_rank=69
a	0	35	28	19	17	94	0	1	3	4	19	4	113	114	5	57	51	29
c	0	26	32	27	19	10	1	0	0	90	2	108	1	0	6	23	18	25
g	0	25	26	18	23	6	0	1	107	2	90	0	0	1	10	18	27	33
t	0	29	29	51	56	5	114	113	5	19	4	3	1	0	94	17	19	28
positions_6nt_m2_shift1 (positions_6nt_m2) 0.791 0.615 11.873 0.619 0.915 2.832 0.899 83 79 18 47 88 90 89 70.571 74 
; oligos_7nt_mkv4_m2 versus positions_6nt_m2; m=9/12; ncol2=18; w=14; offset=-2; strand=D; shift=1; score=70.5714; -mwgTGTTGCACAATcac
; cor=0.791; Ncor=0.615; logoDP=11.873; NIcor=0.619; NsEucl=0.915; SSD=2.832; NSW=0.899; rcor=83; rNcor=79; rlogoDP=18; rNIcor=47; rNsEucl=88; rSSD=90; rNSW=89; rank_mean=70.571; match_rank=74
a	0	12	13	6	4	5	0	0	2	0	37	1	41	41	0	5	26	9
c	0	14	1	7	2	4	0	0	0	42	1	40	0	0	1	24	6	16
g	0	7	8	27	5	31	0	0	39	0	3	0	0	1	3	9	3	9
t	0	9	20	2	31	2	42	42	1	0	1	1	1	0	38	4	7	8
positions_6nt_m4_shift1 (positions_6nt_m4) 0.788 0.613 10.796 0.609 0.917 2.728 0.903 84 80 35 50 86 87 86 72.571 79 
; oligos_7nt_mkv4_m2 versus positions_6nt_m4; m=10/12; ncol2=18; w=14; offset=-2; strand=D; shift=1; score=72.5714; -mbtgATTGCGCAATcav
; cor=0.788; Ncor=0.613; logoDP=10.796; NIcor=0.609; NsEucl=0.917; SSD=2.728; NSW=0.903; rcor=84; rNcor=80; rlogoDP=35; rNIcor=50; rNsEucl=86; rSSD=87; rNSW=86; rank_mean=72.571; match_rank=79
a	0	14	9	6	4	40	0	0	0	3	6	3	46	46	1	5	24	12
c	0	13	13	7	6	3	0	0	0	35	2	43	0	0	2	31	9	12
g	0	10	12	9	31	2	0	0	43	2	35	0	0	0	3	6	7	13
t	0	9	12	24	5	1	46	46	3	6	3	0	0	0	40	4	6	9
oligos_7nt_mkv4_m5_rc_shift4 (oligos_7nt_mkv4_m5_rc) 0.761 0.653 8.569 0.636 0.903 2.684 0.888 94 73 64 46 95 85 95 78.857 88 
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m5_rc; m=11/12; ncol2=12; w=12; offset=1; strand=R; shift=4; score=78.8571; ----kaTTrCGCAAyr--
; cor=0.761; Ncor=0.653; logoDP=8.569; NIcor=0.636; NsEucl=0.903; SSD=2.684; NSW=0.888; rcor=94; rNcor=73; rlogoDP=64; rNIcor=46; rNsEucl=95; rSSD=85; rNSW=95; rank_mean=78.857; match_rank=88
a	0	0	0	0	42	85	3	3	96	2	5	4	168	168	15	46	0	0
c	0	0	0	0	33	28	2	4	2	162	1	150	0	0	43	38	0	0
g	0	0	0	0	45	42	2	13	50	3	165	2	2	2	32	45	0	0
t	0	0	0	0	51	16	164	151	23	4	0	15	1	1	81	42	0	0
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc) 0.806 0.627 5.310 0.292 0.919 2.602 0.907 78 76 80 78 81 84 85 80.286 92 
; oligos_7nt_mkv4_m2 versus positions_7nt_m5_rc; m=12/12; ncol2=18; w=14; offset=-3; strand=R; shift=0; score=80.2857; ymdgTGTTGCACAATcwc
; cor=0.806; Ncor=0.627; logoDP=5.310; NIcor=0.292; NsEucl=0.919; SSD=2.602; NSW=0.907; rcor=78; rNcor=76; rlogoDP=80; rNIcor=78; rNsEucl=81; rSSD=84; rNSW=85; rank_mean=80.286; match_rank=92
a	10	19	14	10	3	6	0	0	2	0	46	0	54	54	1	5	19	9
c	15	17	3	10	2	5	0	0	1	54	2	53	0	0	1	29	10	21
g	11	6	15	29	7	41	0	1	50	0	3	0	0	0	3	12	7	13
t	18	12	22	5	42	2	54	53	1	0	3	1	0	0	49	8	18	11

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift2 ; 15 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)                                 
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=15; shift=2; ncol=18; --rtgATTGCACAATmy-
; Alignment reference
a	0	0	41	31	23	122	1	1	5	0	129	4	148	147	5	40	31	0
c	0	0	30	35	21	8	0	0	0	150	2	143	1	1	18	42	45	0
g	0	0	46	29	89	13	0	0	137	0	15	0	0	1	9	36	36	0
t	0	0	33	55	17	7	149	149	8	0	4	3	1	1	118	32	38	0
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1) 0.985 0.862 11.908 0.864 0.978 0.192 0.993 4 18 17 13 4 4 4 9.143 5 
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=1/14; ncol2=15; w=14; offset=1; strand=D; shift=3; score= 9.1429; ---ytATTGCACAATmcy
; cor=0.985; Ncor=0.862; logoDP=11.908; NIcor=0.864; NsEucl=0.978; SSD=0.192; NSW=0.993; rcor=4; rNcor=18; rlogoDP=17; rNIcor=13; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=9.143; match_rank=5
a	0	0	0	71	70	210	0	2	11	0	253	6	283	282	4	86	69	60
c	0	0	0	78	69	25	0	0	0	282	5	271	3	1	43	76	81	78
g	0	0	0	56	70	36	0	0	260	0	18	0	0	2	22	65	65	62
t	0	0	0	81	77	15	286	284	15	4	10	9	0	1	217	59	71	86
positions_6nt_m5_shift1 (positions_6nt_m5) 0.937 0.878 12.682 0.875 0.957 0.849 0.972 18 11 9 9 17 18 18 14.286 9 
; oligos_6nt_mkv3_m1 versus positions_6nt_m5; m=2/14; ncol2=16; w=15; offset=-1; strand=D; shift=1; score=14.2857; -aktgATTGCACAACay-
; cor=0.937; Ncor=0.878; logoDP=12.682; NIcor=0.875; NsEucl=0.957; SSD=0.849; NSW=0.972; rcor=18; rNcor=11; rlogoDP=9; rNIcor=9; rNsEucl=17; rSSD=18; rNSW=18; rank_mean=14.286; match_rank=9
a	0	31	15	18	11	69	0	0	2	0	74	0	79	79	1	30	14	0
c	0	15	19	7	10	2	0	0	1	79	1	74	0	0	57	17	28	0
g	0	16	23	9	48	7	0	0	74	0	4	0	0	0	5	13	11	0
t	0	17	22	45	10	1	79	79	2	0	0	5	0	0	16	19	26	0
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2) 0.938 0.875 11.941 0.874 0.955 0.785 0.972 16 12 16 10 19 14 17 14.857 11 
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m2; m=3/14; ncol2=14; w=14; offset=1; strand=D; shift=3; score=14.8571; ---wrATTGCACAAcwy-
; cor=0.938; Ncor=0.875; logoDP=11.941; NIcor=0.874; NsEucl=0.955; SSD=0.785; NSW=0.972; rcor=16; rNcor=12; rlogoDP=16; rNIcor=10; rNsEucl=19; rSSD=14; rNSW=17; rank_mean=14.857; match_rank=11
a	0	0	0	72	59	190	1	0	11	1	209	3	233	233	4	90	46	0
c	0	0	0	55	56	14	0	0	2	234	8	223	2	0	153	53	71	0
g	0	0	0	39	63	26	0	1	213	0	9	2	0	0	22	28	54	0
t	0	0	0	69	57	5	234	234	9	0	9	7	0	2	56	64	64	0
positions_7nt_m4_shift1 (positions_7nt_m4) 0.926 0.817 12.457 0.813 0.953 0.998 0.967 19 26 12 17 21 20 19 19.143 13 
; oligos_6nt_mkv3_m1 versus positions_7nt_m4; m=4/14; ncol2=17; w=15; offset=-1; strand=D; shift=1; score=19.1429; -ryTgATTGCACAACtyy
; cor=0.926; Ncor=0.817; logoDP=12.457; NIcor=0.813; NsEucl=0.953; SSD=0.998; NSW=0.967; rcor=19; rNcor=26; rlogoDP=12; rNIcor=17; rNsEucl=21; rSSD=20; rNSW=19; rank_mean=19.143; match_rank=13
a	0	30	15	9	10	58	0	0	0	0	64	0	71	72	1	17	12	15
c	0	11	23	5	9	1	0	0	1	72	2	69	1	0	52	10	24	19
g	0	18	15	7	44	10	0	0	68	0	3	0	0	0	2	9	13	13
t	0	13	19	51	9	3	72	72	3	0	3	3	0	0	17	36	23	25
positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc) 0.976 0.813 10.193 0.606 0.972 0.343 0.989 7 27 46 52 6 7 7 21.714 14 
; oligos_6nt_mkv3_m1 versus positions_6nt_m1_rc; m=5/14; ncol2=18; w=15; offset=-1; strand=R; shift=1; score=21.7143; -awtgATTGCACAATcmt
; cor=0.976; Ncor=0.813; logoDP=10.193; NIcor=0.606; NsEucl=0.972; SSD=0.343; NSW=0.989; rcor=7; rNcor=27; rlogoDP=46; rNIcor=52; rNsEucl=6; rSSD=7; rNSW=7; rank_mean=21.714; match_rank=14
a	0	20	18	4	8	48	0	1	0	0	48	0	55	54	1	13	25	11
c	0	13	11	6	5	1	0	0	0	55	2	52	0	0	4	30	14	13
g	0	9	12	9	36	3	0	0	51	0	3	0	0	0	2	6	7	13
t	0	13	14	36	6	3	55	54	4	0	2	3	0	1	48	6	9	18
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc) 0.939 0.783 9.893 0.607 0.957 0.824 0.973 15 36 52 51 16 17 16 29.000 21 
; oligos_6nt_mkv3_m1 versus positions_6nt_m3_rc; m=6/14; ncol2=18; w=15; offset=-1; strand=R; shift=1; score=     29; -aaytATTGCACAATcat
; cor=0.939; Ncor=0.783; logoDP=9.893; NIcor=0.607; NsEucl=0.957; SSD=0.824; NSW=0.973; rcor=15; rNcor=36; rlogoDP=52; rNIcor=51; rNsEucl=16; rSSD=17; rNSW=16; rank_mean=29.000; match_rank=21
a	0	20	17	9	9	46	0	1	3	0	48	1	53	53	2	11	32	11
c	0	11	12	14	9	5	0	1	1	53	0	51	0	0	2	31	9	13
g	0	9	12	5	6	2	0	0	45	0	4	0	0	0	3	7	5	12
t	0	13	12	25	29	0	53	51	4	0	1	1	0	0	46	4	7	17
oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3) 0.894 0.834 9.841 0.826 0.943 1.296 0.954 32 24 53 16 35 30 31 31.571 22 
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m3; m=7/14; ncol2=14; w=14; offset=0; strand=D; shift=2; score=31.5714; --rwkATTTCACAAym--
; cor=0.894; Ncor=0.834; logoDP=9.841; NIcor=0.826; NsEucl=0.943; SSD=1.296; NSW=0.954; rcor=32; rNcor=24; rlogoDP=53; rNIcor=16; rNsEucl=35; rSSD=30; rNSW=31; rank_mean=31.571; match_rank=22
a	0	0	62	57	19	194	1	5	23	0	176	9	201	195	25	70	0	0
c	0	0	40	46	26	4	0	1	5	210	12	190	4	1	64	58	0	0
g	0	0	69	41	101	10	2	9	33	0	15	2	0	8	32	39	0	0
t	0	0	39	66	64	2	207	195	149	0	7	9	5	6	89	43	0	0
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc) 0.978 0.863 4.036 0.030 0.974 0.308 0.990 6 16 92 98 5 6 5 32.571 23 
; oligos_6nt_mkv3_m1 versus positions_7nt_m1_rc; m=8/14; ncol2=17; w=15; offset=-1; strand=R; shift=1; score=32.5714; -aaTgATTGCACAATchy
; cor=0.978; Ncor=0.863; logoDP=4.036; NIcor=0.030; NsEucl=0.974; SSD=0.308; NSW=0.990; rcor=6; rNcor=16; rlogoDP=92; rNIcor=98; rNsEucl=5; rSSD=6; rNSW=5; rank_mean=32.571; match_rank=23
a	0	24	23	7	9	57	0	1	0	0	66	1	75	75	2	11	19	13
c	0	16	17	6	11	5	0	0	0	75	2	71	0	0	6	43	24	22
g	0	17	18	10	48	8	0	0	69	0	4	0	0	0	1	10	11	17
t	0	18	17	52	7	5	75	74	6	0	3	3	0	0	66	11	21	23
positions_6nt_m4_shift1 (positions_6nt_m4) 0.887 0.739 11.039 0.731 0.943 1.481 0.951 38 50 29 32 34 41 33 36.714 29 
; oligos_6nt_mkv3_m1 versus positions_6nt_m4; m=9/14; ncol2=18; w=15; offset=-1; strand=D; shift=1; score=36.7143; -mbtgATTGCGCAATcav
; cor=0.887; Ncor=0.739; logoDP=11.039; NIcor=0.731; NsEucl=0.943; SSD=1.481; NSW=0.951; rcor=38; rNcor=50; rlogoDP=29; rNIcor=32; rNsEucl=34; rSSD=41; rNSW=33; rank_mean=36.714; match_rank=29
a	0	14	9	6	4	40	0	0	0	3	6	3	46	46	1	5	24	12
c	0	13	13	7	6	3	0	0	0	35	2	43	0	0	2	31	9	12
g	0	10	12	9	31	2	0	0	43	2	35	0	0	0	3	6	7	13
t	0	9	12	24	5	1	46	46	3	6	3	0	0	0	40	4	6	9
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc) 0.879 0.733 10.427 0.729 0.942 1.508 0.950 43 52 41 33 36 43 37 40.714 35 
; oligos_6nt_mkv3_m1 versus positions_7nt_m2_rc; m=10/14; ncol2=18; w=15; offset=-1; strand=R; shift=1; score=40.7143; -wyttATTGCGCAATaar
; cor=0.879; Ncor=0.733; logoDP=10.427; NIcor=0.729; NsEucl=0.942; SSD=1.508; NSW=0.950; rcor=43; rNcor=52; rlogoDP=41; rNIcor=33; rNsEucl=36; rSSD=43; rNSW=37; rank_mean=40.714; match_rank=35
a	0	35	28	19	17	94	0	1	3	4	19	4	113	114	5	57	51	29
c	0	26	32	27	19	10	1	0	0	90	2	108	1	0	6	23	18	25
g	0	25	26	18	23	6	0	1	107	2	90	0	0	1	10	18	27	33
t	0	29	29	51	56	5	114	113	5	19	4	3	1	0	94	17	19	28
oligos_7nt_mkv4_m4_shift4 (oligos_7nt_mkv4_m4) 0.871 0.697 11.183 0.706 0.926 1.557 0.935 50 64 27 39 72 47 60 51.286 51 
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m4; m=11/14; ncol2=12; w=12; offset=2; strand=D; shift=4; score=51.2857; ----krTTGCkCAAyw--
; cor=0.871; Ncor=0.697; logoDP=11.183; NIcor=0.706; NsEucl=0.926; SSD=1.557; NSW=0.935; rcor=50; rNcor=64; rlogoDP=27; rNIcor=39; rNsEucl=72; rSSD=47; rNSW=60; rank_mean=51.286; match_rank=51
a	0	0	0	0	34	80	0	2	1	0	10	4	168	170	11	61	0	0
c	0	0	0	0	33	28	0	4	0	172	3	165	0	1	53	30	0	0
g	0	0	0	0	44	49	0	0	170	0	58	0	3	1	29	32	0	0
t	0	0	0	0	61	15	172	166	1	0	101	3	1	0	79	49	0	0
positions_6nt_m2_shift1 (positions_6nt_m2) 0.832 0.693 12.145 0.706 0.928 2.339 0.922 71 66 14 38 68 74 71 57.429 59 
; oligos_6nt_mkv3_m1 versus positions_6nt_m2; m=12/14; ncol2=18; w=15; offset=-1; strand=D; shift=1; score=57.4286; -mwgTGTTGCACAATcac
; cor=0.832; Ncor=0.693; logoDP=12.145; NIcor=0.706; NsEucl=0.928; SSD=2.339; NSW=0.922; rcor=71; rNcor=66; rlogoDP=14; rNIcor=38; rNsEucl=68; rSSD=74; rNSW=71; rank_mean=57.429; match_rank=59
a	0	12	13	6	4	5	0	0	2	0	37	1	41	41	0	5	26	9
c	0	14	1	7	2	4	0	0	0	42	1	40	0	0	1	24	6	16
g	0	7	8	27	5	31	0	0	39	0	3	0	0	1	3	9	3	9
t	0	9	20	2	31	2	42	42	1	0	1	1	1	0	38	4	7	8
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc) 0.849 0.708 5.348 0.263 0.932 2.064 0.931 64 61 79 80 59 68 63 67.714 72 
; oligos_6nt_mkv3_m1 versus positions_7nt_m5_rc; m=13/14; ncol2=18; w=15; offset=-2; strand=R; shift=0; score=67.7143; ymdgTGTTGCACAATcwc
; cor=0.849; Ncor=0.708; logoDP=5.348; NIcor=0.263; NsEucl=0.932; SSD=2.064; NSW=0.931; rcor=64; rNcor=61; rlogoDP=79; rNIcor=80; rNsEucl=59; rSSD=68; rNSW=63; rank_mean=67.714; match_rank=72
a	10	19	14	10	3	6	0	0	2	0	46	0	54	54	1	5	19	9
c	15	17	3	10	2	5	0	0	1	54	2	53	0	0	1	29	10	21
g	11	6	15	29	7	41	0	1	50	0	3	0	0	0	3	12	7	13
t	18	12	22	5	42	2	54	53	1	0	3	1	0	0	49	8	18	11
oligos_7nt_mkv4_m5_rc_shift4 (oligos_7nt_mkv4_m5_rc) 0.778 0.622 8.561 0.599 0.905 2.578 0.893 88 78 65 54 93 81 92 78.714 87 
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m5_rc; m=14/14; ncol2=12; w=12; offset=2; strand=R; shift=4; score=78.7143; ----kaTTrCGCAAyr--
; cor=0.778; Ncor=0.622; logoDP=8.561; NIcor=0.599; NsEucl=0.905; SSD=2.578; NSW=0.893; rcor=88; rNcor=78; rlogoDP=65; rNIcor=54; rNsEucl=93; rSSD=81; rNSW=92; rank_mean=78.714; match_rank=87
a	0	0	0	0	42	85	3	3	96	2	5	4	168	168	15	46	0	0
c	0	0	0	0	33	28	2	4	2	162	1	150	0	0	43	38	0	0
g	0	0	0	0	45	42	2	13	50	3	165	2	2	2	32	45	0	0
t	0	0	0	0	51	16	164	151	23	4	0	15	1	1	81	42	0	0

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 7 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)                                 
; positions_6nt_m3; m=0 (reference); ncol1=18; shift=0; ncol=19; catgATTGTGCAATartt-
; Alignment reference
a	12	17	7	4	46	0	0	1	1	0	4	51	53	0	29	25	12	13	0
c	16	12	5	7	3	0	0	0	4	0	45	0	0	2	6	5	12	9	0
g	13	13	9	31	2	0	0	51	0	53	1	1	0	5	9	14	12	11	0
t	12	11	32	11	2	53	53	1	48	0	3	1	0	46	9	9	17	20	0
positions_7nt_m1_shift1 (positions_7nt_m1) 0.943 0.890 12.910 0.900 0.963 0.805 0.976 14 8 6 6 13 15 15 11.000 6 
; positions_6nt_m3 versus positions_7nt_m1; m=1/6; ncol2=17; w=17; offset=1; strand=D; shift=1; score=     11; -rdgATTGTGCAATcAtt-
; cor=0.943; Ncor=0.890; logoDP=12.910; NIcor=0.900; NsEucl=0.963; SSD=0.805; NSW=0.976; rcor=14; rNcor=8; rlogoDP=6; rNIcor=6; rNsEucl=13; rSSD=15; rNSW=15; rank_mean=11.000; match_rank=6
a	0	23	21	11	66	0	0	3	3	0	6	74	75	5	7	52	17	18	0
c	0	17	11	10	1	0	0	0	4	0	69	0	0	8	48	10	18	17	0
g	0	22	24	43	6	0	0	71	2	75	0	0	0	5	11	6	17	16	0
t	0	13	19	11	2	75	75	1	66	0	0	1	0	57	9	7	23	24	0
positions_7nt_m2_rc_shift0 (positions_7nt_m2_rc) 0.889 0.889 10.671 0.879 0.952 1.486 0.959 33 9 37 8 23 42 28 25.714 19 
; positions_6nt_m3 versus positions_7nt_m2_rc; m=2/6; ncol2=18; w=18; offset=0; strand=R; shift=0; score=25.7143; wyttATTGCGCAATaart-
; cor=0.889; Ncor=0.889; logoDP=10.671; NIcor=0.879; NsEucl=0.952; SSD=1.486; NSW=0.959; rcor=33; rNcor=9; rlogoDP=37; rNIcor=8; rNsEucl=23; rSSD=42; rNSW=28; rank_mean=25.714; match_rank=19
a	35	28	19	17	94	0	1	3	4	19	4	113	114	5	57	51	29	28	0
c	26	32	27	19	10	1	0	0	90	2	108	1	0	6	23	18	25	25	0
g	25	26	18	23	6	0	1	107	2	90	0	0	1	10	18	27	33	27	0
t	29	29	51	56	5	114	113	5	19	4	3	1	0	94	17	19	28	35	0
positions_6nt_m4_shift0 (positions_6nt_m4) 0.868 0.868 11.350 0.866 0.947 1.811 0.950 52 14 24 12 30 59 38 32.714 25 
; positions_6nt_m3 versus positions_6nt_m4; m=3/6; ncol2=18; w=18; offset=0; strand=D; shift=0; score=32.7143; mbtgATTGCGCAATcavk-
; cor=0.868; Ncor=0.868; logoDP=11.350; NIcor=0.866; NsEucl=0.947; SSD=1.811; NSW=0.950; rcor=52; rNcor=14; rlogoDP=24; rNIcor=12; rNsEucl=30; rSSD=59; rNSW=38; rank_mean=32.714; match_rank=25
a	14	9	6	4	40	0	0	0	3	6	3	46	46	1	5	24	12	9	0
c	13	13	7	6	3	0	0	0	35	2	43	0	0	2	31	9	12	10	0
g	10	12	9	31	2	0	0	43	2	35	0	0	0	3	6	7	13	13	0
t	9	12	24	5	1	46	46	3	6	3	0	0	0	40	4	6	9	14	0
positions_7nt_m5_shift1 (positions_7nt_m5) 0.873 0.782 12.775 0.796 0.944 1.800 0.947 48 37 8 21 33 58 45 35.714 26 
; positions_6nt_m3 versus positions_7nt_m5; m=4/6; ncol2=18; w=17; offset=1; strand=D; shift=1; score=35.7143; -gwgATTGTGCAACAchkr
; cor=0.873; Ncor=0.782; logoDP=12.775; NIcor=0.796; NsEucl=0.944; SSD=1.800; NSW=0.947; rcor=48; rNcor=37; rlogoDP=8; rNIcor=21; rNsEucl=33; rSSD=58; rNSW=45; rank_mean=35.714; match_rank=26
a	0	11	18	8	49	0	0	1	3	0	1	53	54	2	42	5	22	12	18
c	0	13	7	12	3	0	0	0	3	0	50	1	0	41	7	29	15	6	11
g	0	21	10	29	1	0	0	53	2	54	1	0	0	5	2	10	3	17	15
t	0	9	19	5	1	54	54	0	46	0	2	0	0	6	3	10	14	19	10
positions_6nt_m5_rc_shift2 (positions_6nt_m5_rc) 0.864 0.768 5.190 0.259 0.939 1.883 0.941 56 42 82 81 44 63 52 60.000 64 
; positions_6nt_m3 versus positions_6nt_m5_rc; m=5/6; ncol2=16; w=16; offset=2; strand=R; shift=2; score=     60; --rtGTTGTGCAATcamt-
; cor=0.864; Ncor=0.768; logoDP=5.190; NIcor=0.259; NsEucl=0.939; SSD=1.883; NSW=0.941; rcor=56; rNcor=42; rlogoDP=82; rNIcor=81; rNsEucl=44; rSSD=63; rNSW=52; rank_mean=60.000; match_rank=64
a	0	0	26	19	16	0	0	5	0	0	2	79	79	1	10	45	22	17	0
c	0	0	11	13	5	0	0	0	4	0	74	0	0	7	48	9	23	16	0
g	0	0	28	17	57	0	0	74	1	79	1	0	0	2	10	7	19	15	0
t	0	0	14	30	1	79	79	0	74	0	2	0	0	69	11	18	15	31	0
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc) 0.848 0.801 4.003 0.055 0.939 2.118 0.938 66 31 93 92 43 71 56 64.571 70 
; positions_6nt_m3 versus positions_7nt_m4_rc; m=6/6; ncol2=17; w=17; offset=1; strand=R; shift=1; score=64.5714; -rraGTTGTGCAATcAry-
; cor=0.848; Ncor=0.801; logoDP=4.003; NIcor=0.055; NsEucl=0.939; SSD=2.118; NSW=0.938; rcor=66; rNcor=31; rlogoDP=93; rNIcor=92; rNsEucl=43; rSSD=71; rNSW=56; rank_mean=64.571; match_rank=70
a	0	25	23	36	17	0	0	3	3	0	3	72	72	3	9	51	19	13	0
c	0	13	13	9	2	0	0	0	3	0	68	0	0	10	44	7	15	18	0
g	0	19	24	10	52	0	1	69	2	72	1	0	0	1	9	5	23	11	0
t	0	15	12	17	1	72	71	0	64	0	0	0	0	58	10	9	15	30	0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift3 ; 14 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor 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=15; shift=3; ncol=18; ---ytATTGCACAATmcy
; Alignment reference
a	0	0	0	71	70	210	0	2	11	0	253	6	283	282	4	86	69	60
c	0	0	0	78	69	25	0	0	0	282	5	271	3	1	43	76	81	78
g	0	0	0	56	70	36	0	0	260	0	18	0	0	2	22	65	65	62
t	0	0	0	81	77	15	286	284	15	4	10	9	0	1	217	59	71	86
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2) 0.954 0.890 11.864 0.887 0.962 0.566 0.980 12 7 19 7 15 10 11 11.571 7 
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m2; m=1/13; ncol2=14; w=14; offset=0; strand=D; shift=3; score=11.5714; ---wrATTGCACAAcwy-
; cor=0.954; Ncor=0.890; logoDP=11.864; NIcor=0.887; NsEucl=0.962; SSD=0.566; NSW=0.980; rcor=12; rNcor=7; rlogoDP=19; rNIcor=7; rNsEucl=15; rSSD=10; rNSW=11; rank_mean=11.571; match_rank=7
a	0	0	0	72	59	190	1	0	11	1	209	3	233	233	4	90	46	0
c	0	0	0	55	56	14	0	0	2	234	8	223	2	0	153	53	71	0
g	0	0	0	39	63	26	0	1	213	0	9	2	0	0	22	28	54	0
t	0	0	0	69	57	5	234	234	9	0	9	7	0	2	56	64	64	0
positions_7nt_m4_shift1 (positions_7nt_m4) 0.911 0.804 12.337 0.802 0.949 1.181 0.961 24 30 13 20 28 24 25 23.429 15 
; oligos_7nt_mkv4_m1 versus positions_7nt_m4; m=2/13; ncol2=17; w=15; offset=-2; strand=D; shift=1; score=23.4286; -ryTgATTGCACAACtyy
; cor=0.911; Ncor=0.804; logoDP=12.337; NIcor=0.802; NsEucl=0.949; SSD=1.181; NSW=0.961; rcor=24; rNcor=30; rlogoDP=13; rNIcor=20; rNsEucl=28; rSSD=24; rNSW=25; rank_mean=23.429; match_rank=15
a	0	30	15	9	10	58	0	0	0	0	64	0	71	72	1	17	12	15
c	0	11	23	5	9	1	0	0	1	72	2	69	1	0	52	10	24	19
g	0	18	15	7	44	10	0	0	68	0	3	0	0	0	2	9	13	13
t	0	13	19	51	9	3	72	72	3	0	3	3	0	0	17	36	23	25
positions_6nt_m5_shift1 (positions_6nt_m5) 0.924 0.761 12.548 0.758 0.949 1.007 0.964 20 43 11 27 27 21 22 24.429 17 
; oligos_7nt_mkv4_m1 versus positions_6nt_m5; m=3/13; ncol2=16; w=14; offset=-2; strand=D; shift=1; score=24.4286; -aktgATTGCACAACay-
; cor=0.924; Ncor=0.761; logoDP=12.548; NIcor=0.758; NsEucl=0.949; SSD=1.007; NSW=0.964; rcor=20; rNcor=43; rlogoDP=11; rNIcor=27; rNsEucl=27; rSSD=21; rNSW=22; rank_mean=24.429; match_rank=17
a	0	31	15	18	11	69	0	0	2	0	74	0	79	79	1	30	14	0
c	0	15	19	7	10	2	0	0	1	79	1	74	0	0	57	17	28	0
g	0	16	23	9	48	7	0	0	74	0	4	0	0	0	5	13	11	0
t	0	17	22	45	10	1	79	79	2	0	0	5	0	0	16	19	26	0
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc) 0.961 0.801 9.774 0.589 0.966 0.533 0.982 9 32 55 57 9 9 8 25.571 18 
; oligos_7nt_mkv4_m1 versus positions_6nt_m3_rc; m=4/13; ncol2=18; w=15; offset=-2; strand=R; shift=1; score=25.5714; -aaytATTGCACAATcat
; cor=0.961; Ncor=0.801; logoDP=9.774; NIcor=0.589; NsEucl=0.966; SSD=0.533; NSW=0.982; rcor=9; rNcor=32; rlogoDP=55; rNIcor=57; rNsEucl=9; rSSD=9; rNSW=8; rank_mean=25.571; match_rank=18
a	0	20	17	9	9	46	0	1	3	0	48	1	53	53	2	11	32	11
c	0	11	12	14	9	5	0	1	1	53	0	51	0	0	2	31	9	13
g	0	9	12	5	6	2	0	0	45	0	4	0	0	0	3	7	5	12
t	0	13	12	25	29	0	53	51	4	0	1	1	0	0	46	4	7	17
positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc) 0.954 0.795 10.065 0.590 0.962 0.649 0.978 13 33 48 56 14 13 13 27.143 20 
; oligos_7nt_mkv4_m1 versus positions_6nt_m1_rc; m=5/13; ncol2=18; w=15; offset=-2; strand=R; shift=1; score=27.1429; -awtgATTGCACAATcmt
; cor=0.954; Ncor=0.795; logoDP=10.065; NIcor=0.590; NsEucl=0.962; SSD=0.649; NSW=0.978; rcor=13; rNcor=33; rlogoDP=48; rNIcor=56; rNsEucl=14; rSSD=13; rNSW=13; rank_mean=27.143; match_rank=20
a	0	20	18	4	8	48	0	1	0	0	48	0	55	54	1	13	25	11
c	0	13	11	6	5	1	0	0	0	55	2	52	0	0	4	30	14	13
g	0	9	12	9	36	3	0	0	51	0	3	0	0	0	2	6	7	13
t	0	13	14	36	6	3	55	54	4	0	2	3	0	1	48	6	9	18
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc) 0.955 0.843 4.086 0.049 0.963 0.616 0.979 10 23 90 93 12 11 12 35.857 27 
; oligos_7nt_mkv4_m1 versus positions_7nt_m1_rc; m=6/13; ncol2=17; w=15; offset=-2; strand=R; shift=1; score=35.8571; -aaTgATTGCACAATchy
; cor=0.955; Ncor=0.843; logoDP=4.086; NIcor=0.049; NsEucl=0.963; SSD=0.616; NSW=0.979; rcor=10; rNcor=23; rlogoDP=90; rNIcor=93; rNsEucl=12; rSSD=11; rNSW=12; rank_mean=35.857; match_rank=27
a	0	24	23	7	9	57	0	1	0	0	66	1	75	75	2	11	19	13
c	0	16	17	6	11	5	0	0	0	75	2	71	0	0	6	43	24	22
g	0	17	18	10	48	8	0	0	69	0	4	0	0	0	1	10	11	17
t	0	18	17	52	7	5	75	74	6	0	3	3	0	0	66	11	21	23
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc) 0.889 0.740 10.332 0.735 0.945 1.357 0.955 34 47 43 30 32 35 30 35.857 28 
; oligos_7nt_mkv4_m1 versus positions_7nt_m2_rc; m=7/13; ncol2=18; w=15; offset=-2; strand=R; shift=1; score=35.8571; -wyttATTGCGCAATaar
; cor=0.889; Ncor=0.740; logoDP=10.332; NIcor=0.735; NsEucl=0.945; SSD=1.357; NSW=0.955; rcor=34; rNcor=47; rlogoDP=43; rNIcor=30; rNsEucl=32; rSSD=35; rNSW=30; rank_mean=35.857; match_rank=28
a	0	35	28	19	17	94	0	1	3	4	19	4	113	114	5	57	51	29
c	0	26	32	27	19	10	1	0	0	90	2	108	1	0	6	23	18	25
g	0	25	26	18	23	6	0	1	107	2	90	0	0	1	10	18	27	33
t	0	29	29	51	56	5	114	113	5	19	4	3	1	0	94	17	19	28
positions_6nt_m2_shift1 (positions_6nt_m2) 0.874 0.728 12.091 0.735 0.938 1.724 0.943 47 53 15 31 45 52 50 41.857 37 
; oligos_7nt_mkv4_m1 versus positions_6nt_m2; m=8/13; ncol2=18; w=15; offset=-2; strand=D; shift=1; score=41.8571; -mwgTGTTGCACAATcac
; cor=0.874; Ncor=0.728; logoDP=12.091; NIcor=0.735; NsEucl=0.938; SSD=1.724; NSW=0.943; rcor=47; rNcor=53; rlogoDP=15; rNIcor=31; rNsEucl=45; rSSD=52; rNSW=50; rank_mean=41.857; match_rank=37
a	0	12	13	6	4	5	0	0	2	0	37	1	41	41	0	5	26	9
c	0	14	1	7	2	4	0	0	0	42	1	40	0	0	1	24	6	16
g	0	7	8	27	5	31	0	0	39	0	3	0	0	1	3	9	3	9
t	0	9	20	2	31	2	42	42	1	0	1	1	1	0	38	4	7	8
oligos_7nt_mkv4_m3_shift2 (oligos_7nt_mkv4_m3) 0.887 0.721 9.655 0.712 0.937 1.326 0.949 39 54 56 35 47 31 39 43.000 41 
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m3; m=9/13; ncol2=14; w=13; offset=-1; strand=D; shift=2; score=     43; --rwkATTTCACAAym--
; cor=0.887; Ncor=0.721; logoDP=9.655; NIcor=0.712; NsEucl=0.937; SSD=1.326; NSW=0.949; rcor=39; rNcor=54; rlogoDP=56; rNIcor=35; rNsEucl=47; rSSD=31; rNSW=39; rank_mean=43.000; match_rank=41
a	0	0	62	57	19	194	1	5	23	0	176	9	201	195	25	70	0	0
c	0	0	40	46	26	4	0	1	5	210	12	190	4	1	64	58	0	0
g	0	0	69	41	101	10	2	9	33	0	15	2	0	8	32	39	0	0
t	0	0	39	66	64	2	207	195	149	0	7	9	5	6	89	43	0	0
oligos_7nt_mkv4_m4_shift4 (oligos_7nt_mkv4_m4) 0.886 0.708 11.132 0.717 0.932 1.337 0.944 41 60 28 34 60 33 47 43.286 42 
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4; m=10/13; ncol2=12; w=12; offset=1; strand=D; shift=4; score=43.2857; ----krTTGCkCAAyw--
; cor=0.886; Ncor=0.708; logoDP=11.132; NIcor=0.717; NsEucl=0.932; SSD=1.337; NSW=0.944; rcor=41; rNcor=60; rlogoDP=28; rNIcor=34; rNsEucl=60; rSSD=33; rNSW=47; rank_mean=43.286; match_rank=42
a	0	0	0	0	34	80	0	2	1	0	10	4	168	170	11	61	0	0
c	0	0	0	0	33	28	0	4	0	172	3	165	0	1	53	30	0	0
g	0	0	0	0	44	49	0	0	170	0	58	0	3	1	29	32	0	0
t	0	0	0	0	61	15	172	166	1	0	101	3	1	0	79	49	0	0
positions_6nt_m4_shift1 (positions_6nt_m4) 0.855 0.712 10.882 0.708 0.936 1.868 0.938 59 57 32 37 52 61 55 50.429 50 
; oligos_7nt_mkv4_m1 versus positions_6nt_m4; m=11/13; ncol2=18; w=15; offset=-2; strand=D; shift=1; score=50.4286; -mbtgATTGCGCAATcav
; cor=0.855; Ncor=0.712; logoDP=10.882; NIcor=0.708; NsEucl=0.936; SSD=1.868; NSW=0.938; rcor=59; rNcor=57; rlogoDP=32; rNIcor=37; rNsEucl=52; rSSD=61; rNSW=55; rank_mean=50.429; match_rank=50
a	0	14	9	6	4	40	0	0	0	3	6	3	46	46	1	5	24	12
c	0	13	13	7	6	3	0	0	0	35	2	43	0	0	2	31	9	12
g	0	10	12	9	31	2	0	0	43	2	35	0	0	0	3	6	7	13
t	0	9	12	24	5	1	46	46	3	6	3	0	0	0	40	4	6	9
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc) 0.887 0.739 5.268 0.289 0.942 1.535 0.949 40 51 81 79 38 45 41 53.571 54 
; oligos_7nt_mkv4_m1 versus positions_7nt_m5_rc; m=12/13; ncol2=18; w=15; offset=-3; strand=R; shift=0; score=53.5714; ymdgTGTTGCACAATcwc
; cor=0.887; Ncor=0.739; logoDP=5.268; NIcor=0.289; NsEucl=0.942; SSD=1.535; NSW=0.949; rcor=40; rNcor=51; rlogoDP=81; rNIcor=79; rNsEucl=38; rSSD=45; rNSW=41; rank_mean=53.571; match_rank=54
a	10	19	14	10	3	6	0	0	2	0	46	0	54	54	1	5	19	9
c	15	17	3	10	2	5	0	0	1	54	2	53	0	0	1	29	10	21
g	11	6	15	29	7	41	0	1	50	0	3	0	0	0	3	12	7	13
t	18	12	22	5	42	2	54	53	1	0	3	1	0	0	49	8	18	11
oligos_7nt_mkv4_m5_rc_shift4 (oligos_7nt_mkv4_m5_rc) 0.783 0.626 8.517 0.610 0.908 2.435 0.899 85 77 66 49 92 76 90 76.429 83 
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m5_rc; m=13/13; ncol2=12; w=12; offset=1; strand=R; shift=4; score=76.4286; ----kaTTrCGCAAyr--
; cor=0.783; Ncor=0.626; logoDP=8.517; NIcor=0.610; NsEucl=0.908; SSD=2.435; NSW=0.899; rcor=85; rNcor=77; rlogoDP=66; rNIcor=49; rNsEucl=92; rSSD=76; rNSW=90; rank_mean=76.429; match_rank=83
a	0	0	0	0	42	85	3	3	96	2	5	4	168	168	15	46	0	0
c	0	0	0	0	33	28	2	4	2	162	1	150	0	0	43	38	0	0
g	0	0	0	0	45	42	2	13	50	3	165	2	2	2	32	45	0	0
t	0	0	0	0	51	16	164	151	23	4	0	15	1	1	81	42	0	0

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 6 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor 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=18; shift=0; ncol=19; mbtgATTGCGCAATcavk-
; Alignment reference
a	14	9	6	4	40	0	0	0	3	6	3	46	46	1	5	24	12	9	0
c	13	13	7	6	3	0	0	0	35	2	43	0	0	2	31	9	12	10	0
g	10	12	9	31	2	0	0	43	2	35	0	0	0	3	6	7	13	13	0
t	9	12	24	5	1	46	46	3	6	3	0	0	0	40	4	6	9	14	0
positions_7nt_m2_rc_shift0 (positions_7nt_m2_rc) 0.937 0.937 10.849 0.946 0.964 0.820 0.977 17 3 33 2 10 16 14 13.571 8 
; positions_6nt_m4 versus positions_7nt_m2_rc; m=1/5; ncol2=18; w=18; offset=0; strand=R; shift=0; score=13.5714; wyttATTGCGCAATaart-
; cor=0.937; Ncor=0.937; logoDP=10.849; NIcor=0.946; NsEucl=0.964; SSD=0.820; NSW=0.977; rcor=17; rNcor=3; rlogoDP=33; rNIcor=2; rNsEucl=10; rSSD=16; rNSW=14; rank_mean=13.571; match_rank=8
a	35	28	19	17	94	0	1	3	4	19	4	113	114	5	57	51	29	28	0
c	26	32	27	19	10	1	0	0	90	2	108	1	0	6	23	18	25	25	0
g	25	26	18	23	6	0	1	107	2	90	0	0	1	10	18	27	33	27	0
t	29	29	51	56	5	114	113	5	19	4	3	1	0	94	17	19	28	35	0
positions_7nt_m1_rc_shift0 (positions_7nt_m1_rc) 0.899 0.849 4.330 0.030 0.951 1.387 0.959 28 22 84 97 26 37 27 45.857 45 
; positions_6nt_m4 versus positions_7nt_m1_rc; m=2/5; ncol2=17; w=17; offset=0; strand=R; shift=0; score=45.8571; aaTgATTGCACAATchy--
; cor=0.899; Ncor=0.849; logoDP=4.330; NIcor=0.030; NsEucl=0.951; SSD=1.387; NSW=0.959; rcor=28; rNcor=22; rlogoDP=84; rNIcor=97; rNsEucl=26; rSSD=37; rNSW=27; rank_mean=45.857; match_rank=45
a	24	23	7	9	57	0	1	0	0	66	1	75	75	2	11	19	13	0	0
c	16	17	6	11	5	0	0	0	75	2	71	0	0	6	43	24	22	0	0
g	17	18	10	48	8	0	0	69	0	4	0	0	0	1	10	11	17	0	0
t	18	17	52	7	5	75	74	6	0	3	3	0	0	66	11	21	23	0	0
positions_7nt_m5_shift1 (positions_7nt_m5) 0.750 0.671 11.477 0.679 0.922 3.481 0.898 98 69 23 41 75 98 91 70.714 75 
; positions_6nt_m4 versus positions_7nt_m5; m=3/5; ncol2=18; w=17; offset=1; strand=D; shift=1; score=70.7143; -gwgATTGTGCAACAchkr
; cor=0.750; Ncor=0.671; logoDP=11.477; NIcor=0.679; NsEucl=0.922; SSD=3.481; NSW=0.898; rcor=98; rNcor=69; rlogoDP=23; rNIcor=41; rNsEucl=75; rSSD=98; rNSW=91; rank_mean=70.714; match_rank=75
a	0	11	18	8	49	0	0	1	3	0	1	53	54	2	42	5	22	12	18
c	0	13	7	12	3	0	0	0	3	0	50	1	0	41	7	29	15	6	11
g	0	21	10	29	1	0	0	53	2	54	1	0	0	5	2	10	3	17	15
t	0	9	19	5	1	54	54	0	46	0	2	0	0	6	3	10	14	19	10
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc) 0.792 0.748 4.265 0.076 0.930 2.845 0.916 81 45 85 88 63 91 78 75.857 82 
; positions_6nt_m4 versus positions_7nt_m4_rc; m=4/5; ncol2=17; w=17; offset=1; strand=R; shift=1; score=75.8571; -rraGTTGTGCAATcAry-
; cor=0.792; Ncor=0.748; logoDP=4.265; NIcor=0.076; NsEucl=0.930; SSD=2.845; NSW=0.916; rcor=81; rNcor=45; rlogoDP=85; rNIcor=88; rNsEucl=63; rSSD=91; rNSW=78; rank_mean=75.857; match_rank=82
a	0	25	23	36	17	0	0	3	3	0	3	72	72	3	9	51	19	13	0
c	0	13	13	9	2	0	0	0	3	0	68	0	0	10	44	7	15	18	0
g	0	19	24	10	52	0	1	69	2	72	1	0	0	1	9	5	23	11	0
t	0	15	12	17	1	72	71	0	64	0	0	0	0	58	10	9	15	30	0
positions_6nt_m5_rc_shift2 (positions_6nt_m5_rc) 0.801 0.712 3.841 0.094 0.927 2.701 0.916 80 58 96 86 69 86 79 79.143 89 
; positions_6nt_m4 versus positions_6nt_m5_rc; m=5/5; ncol2=16; w=16; offset=2; strand=R; shift=2; score=79.1429; --rtGTTGTGCAATcamt-
; cor=0.801; Ncor=0.712; logoDP=3.841; NIcor=0.094; NsEucl=0.927; SSD=2.701; NSW=0.916; rcor=80; rNcor=58; rlogoDP=96; rNIcor=86; rNsEucl=69; rSSD=86; rNSW=79; rank_mean=79.143; match_rank=89
a	0	0	26	19	16	0	0	5	0	0	2	79	79	1	10	45	22	17	0
c	0	0	11	13	5	0	0	0	4	0	74	0	0	7	48	9	23	16	0
g	0	0	28	17	57	0	0	74	1	79	1	0	0	2	10	7	19	15	0
t	0	0	14	30	1	79	79	0	74	0	2	0	0	69	11	18	15	31	0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift1 ; 5 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_6nt_m2_shift1 (positions_6nt_m2)                                 
; positions_6nt_m2; m=0 (reference); ncol1=18; shift=1; ncol=19; -mwgTGTTGCACAATcacw
; Alignment reference
a	0	12	13	6	4	5	0	0	2	0	37	1	41	41	0	5	26	9	15
c	0	14	1	7	2	4	0	0	0	42	1	40	0	0	1	24	6	16	8
g	0	7	8	27	5	31	0	0	39	0	3	0	0	1	3	9	3	9	7
t	0	9	20	2	31	2	42	42	1	0	1	1	1	0	38	4	7	8	12
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc) 0.989 0.885 6.110 0.332 0.983 0.163 0.995 2 10 73 76 2 2 2 23.857 16 
; positions_6nt_m2 versus positions_7nt_m5_rc; m=1/4; ncol2=18; w=17; offset=-1; strand=R; shift=0; score=23.8571; ymdgTGTTGCACAATcwc-
; cor=0.989; Ncor=0.885; logoDP=6.110; NIcor=0.332; NsEucl=0.983; SSD=0.163; NSW=0.995; rcor=2; rNcor=10; rlogoDP=73; rNIcor=76; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=23.857; match_rank=16
a	10	19	14	10	3	6	0	0	2	0	46	0	54	54	1	5	19	9	0
c	15	17	3	10	2	5	0	0	1	54	2	53	0	0	1	29	10	21	0
g	11	6	15	29	7	41	0	1	50	0	3	0	0	0	3	12	7	13	0
t	18	12	22	5	42	2	54	53	1	0	3	1	0	0	49	8	18	11	0
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc) 0.872 0.872 10.021 0.598 0.947 1.845 0.949 49 13 49 55 31 60 42 42.714 38 
; positions_6nt_m2 versus positions_6nt_m3_rc; m=2/4; ncol2=18; w=18; offset=0; strand=R; shift=1; score=42.7143; -aaytATTGCACAATcatg
; cor=0.872; Ncor=0.872; logoDP=10.021; NIcor=0.598; NsEucl=0.947; SSD=1.845; NSW=0.949; rcor=49; rNcor=13; rlogoDP=49; rNIcor=55; rNsEucl=31; rSSD=60; rNSW=42; rank_mean=42.714; match_rank=38
a	0	20	17	9	9	46	0	1	3	0	48	1	53	53	2	11	32	11	12
c	0	11	12	14	9	5	0	1	1	53	0	51	0	0	2	31	9	13	13
g	0	9	12	5	6	2	0	0	45	0	4	0	0	0	3	7	5	12	16
t	0	13	12	25	29	0	53	51	4	0	1	1	0	0	46	4	7	17	12
positions_7nt_m2_shift1 (positions_7nt_m2) 0.776 0.776 10.549 0.787 0.931 3.067 0.915 89 39 39 23 61 96 80 61.000 66 
; positions_6nt_m2 versus positions_7nt_m2; m=3/4; ncol2=18; w=18; offset=0; strand=D; shift=1; score=     61; -ayttATTGCGCAATaarw
; cor=0.776; Ncor=0.776; logoDP=10.549; NIcor=0.787; NsEucl=0.931; SSD=3.067; NSW=0.915; rcor=89; rNcor=39; rlogoDP=39; rNIcor=23; rNsEucl=61; rSSD=96; rNSW=80; rank_mean=61.000; match_rank=66
a	0	35	28	19	17	94	0	1	3	4	19	5	113	114	5	56	51	29	29
c	0	27	33	27	18	10	1	0	0	90	2	107	1	0	6	23	18	26	25
g	0	25	25	18	23	6	0	1	108	2	90	0	0	1	10	19	27	32	26
t	0	28	29	51	57	5	114	113	4	19	4	3	1	0	94	17	19	28	35
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc) 0.823 0.777 4.092 0.038 0.934 2.554 0.925 76 38 89 95 56 79 70 71.857 77 
; positions_6nt_m2 versus positions_7nt_m1_rc; m=4/4; ncol2=17; w=17; offset=0; strand=R; shift=1; score=71.8571; -aaTgATTGCACAATchy-
; cor=0.823; Ncor=0.777; logoDP=4.092; NIcor=0.038; NsEucl=0.934; SSD=2.554; NSW=0.925; rcor=76; rNcor=38; rlogoDP=89; rNIcor=95; rNsEucl=56; rSSD=79; rNSW=70; rank_mean=71.857; match_rank=77
a	0	24	23	7	9	57	0	1	0	0	66	1	75	75	2	11	19	13	0
c	0	16	17	6	11	5	0	0	0	75	2	71	0	0	6	43	24	22	0
g	0	17	18	10	48	8	0	0	69	0	4	0	0	0	1	10	11	17	0
t	0	18	17	52	7	5	75	74	6	0	3	3	0	0	66	11	21	23	0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift1 ; 4 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m1_shift1 (positions_7nt_m1)                                 
; positions_7nt_m1; m=0 (reference); ncol1=17; shift=1; ncol=18; -rdgATTGTGCAATcAtt
; Alignment reference
a	0	23	21	11	66	0	0	3	3	0	6	74	75	5	7	52	17	18
c	0	17	11	10	1	0	0	0	4	0	69	0	0	8	48	10	18	17
g	0	22	24	43	6	0	0	71	2	75	0	0	0	5	11	6	17	16
t	0	13	19	11	2	75	75	1	66	0	0	1	0	57	9	7	23	24
positions_7nt_m4_rc_shift1 (positions_7nt_m4_rc) 0.913 0.913 4.194 0.076 0.954 1.218 0.964 23 5 88 89 20 26 21 38.857 31 
; positions_7nt_m1 versus positions_7nt_m4_rc; m=1/3; ncol2=17; w=17; offset=0; strand=R; shift=1; score=38.8571; -rraGTTGTGCAATcAry
; cor=0.913; Ncor=0.913; logoDP=4.194; NIcor=0.076; NsEucl=0.954; SSD=1.218; NSW=0.964; rcor=23; rNcor=5; rlogoDP=88; rNIcor=89; rNsEucl=20; rSSD=26; rNSW=21; rank_mean=38.857; match_rank=31
a	0	25	23	36	17	0	0	3	3	0	3	72	72	3	9	51	19	13
c	0	13	13	9	2	0	0	0	3	0	68	0	0	10	44	7	15	18
g	0	19	24	10	52	0	1	69	2	72	1	0	0	1	9	5	23	11
t	0	15	12	17	1	72	71	0	64	0	0	0	0	58	10	9	15	30
positions_7nt_m2_shift0 (positions_7nt_m2) 0.853 0.806 10.909 0.809 0.942 1.955 0.942 60 29 31 18 37 66 51 41.714 36 
; positions_7nt_m1 versus positions_7nt_m2; m=2/3; ncol2=18; w=17; offset=-1; strand=D; shift=0; score=41.7143; ayttATTGCGCAATaarw
; cor=0.853; Ncor=0.806; logoDP=10.909; NIcor=0.809; NsEucl=0.942; SSD=1.955; NSW=0.942; rcor=60; rNcor=29; rlogoDP=31; rNIcor=18; rNsEucl=37; rSSD=66; rNSW=51; rank_mean=41.714; match_rank=36
a	35	28	19	17	94	0	1	3	4	19	5	113	114	5	56	51	29	29
c	27	33	27	18	10	1	0	0	90	2	107	1	0	6	23	18	26	25
g	25	25	18	23	6	0	1	108	2	90	0	0	1	10	19	27	32	26
t	28	29	51	57	5	114	113	4	19	4	3	1	0	94	17	19	28	35
positions_7nt_m5_shift1 (positions_7nt_m5) 0.838 0.792 13.109 0.809 0.937 2.306 0.932 69 35 3 19 50 73 61 44.286 44 
; positions_7nt_m1 versus positions_7nt_m5; m=3/3; ncol2=18; w=17; offset=0; strand=D; shift=1; score=44.2857; -gwgATTGTGCAACAchk
; cor=0.838; Ncor=0.792; logoDP=13.109; NIcor=0.809; NsEucl=0.937; SSD=2.306; NSW=0.932; rcor=69; rNcor=35; rlogoDP=3; rNIcor=19; rNsEucl=50; rSSD=73; rNSW=61; rank_mean=44.286; match_rank=44
a	0	11	18	8	49	0	0	1	3	0	1	53	54	2	42	5	22	12
c	0	13	7	12	3	0	0	0	3	0	50	1	0	41	7	29	15	6
g	0	21	10	29	1	0	0	53	2	54	1	0	0	5	2	10	3	17
t	0	9	19	5	1	54	54	0	46	0	2	0	0	6	3	10	14	19

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift1 ; 10 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)                                 
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=14; shift=1; ncol=18; -rwkATTTCACAAym---
; Alignment reference
a	0	62	57	19	194	1	5	23	0	176	9	201	195	25	70	0	0	0
c	0	40	46	26	4	0	1	5	210	12	190	4	1	64	58	0	0	0
g	0	69	41	101	10	2	9	33	0	15	2	0	8	32	39	0	0	0
t	0	39	66	64	2	207	195	149	0	7	9	5	6	89	43	0	0	0
positions_6nt_m5_shift0 (positions_6nt_m5) 0.881 0.770 10.566 0.766 0.937 1.536 0.945 42 40 38 24 46 46 46 40.286 33 
; oligos_7nt_mkv4_m3 versus positions_6nt_m5; m=1/9; ncol2=16; w=14; offset=-1; strand=D; shift=0; score=40.2857; aktgATTGCACAACay--
; cor=0.881; Ncor=0.770; logoDP=10.566; NIcor=0.766; NsEucl=0.937; SSD=1.536; NSW=0.945; rcor=42; rNcor=40; rlogoDP=38; rNIcor=24; rNsEucl=46; rSSD=46; rNSW=46; rank_mean=40.286; match_rank=33
a	31	15	18	11	69	0	0	2	0	74	0	79	79	1	30	14	0	0
c	15	19	7	10	2	0	0	1	79	1	74	0	0	57	17	28	0	0
g	16	23	9	48	7	0	0	74	0	4	0	0	0	5	13	11	0	0
t	17	22	45	10	1	79	79	2	0	0	5	0	0	16	19	26	0	0
positions_7nt_m4_shift0 (positions_7nt_m4) 0.861 0.709 10.221 0.702 0.932 1.788 0.936 57 59 45 40 58 55 58 53.143 53 
; oligos_7nt_mkv4_m3 versus positions_7nt_m4; m=2/9; ncol2=17; w=14; offset=-1; strand=D; shift=0; score=53.1429; ryTgATTGCACAACtyy-
; cor=0.861; Ncor=0.709; logoDP=10.221; NIcor=0.702; NsEucl=0.932; SSD=1.788; NSW=0.936; rcor=57; rNcor=59; rlogoDP=45; rNIcor=40; rNsEucl=58; rSSD=55; rNSW=58; rank_mean=53.143; match_rank=53
a	30	15	9	10	58	0	0	0	0	64	0	71	72	1	17	12	15	0
c	11	23	5	9	1	0	0	1	72	2	69	1	0	52	10	24	19	0
g	18	15	7	44	10	0	0	68	0	3	0	0	0	2	9	13	13	0
t	13	19	51	9	3	72	72	3	0	3	3	0	0	17	36	23	25	0
positions_6nt_m3_rc_shift0 (positions_6nt_m3_rc) 0.875 0.681 7.525 0.460 0.936 1.598 0.943 45 67 71 75 51 48 49 58.000 60 
; oligos_7nt_mkv4_m3 versus positions_6nt_m3_rc; m=3/9; ncol2=18; w=14; offset=-1; strand=R; shift=0; score=     58; aaytATTGCACAATcatg
; cor=0.875; Ncor=0.681; logoDP=7.525; NIcor=0.460; NsEucl=0.936; SSD=1.598; NSW=0.943; rcor=45; rNcor=67; rlogoDP=71; rNIcor=75; rNsEucl=51; rSSD=48; rNSW=49; rank_mean=58.000; match_rank=60
a	20	17	9	9	46	0	1	3	0	48	1	53	53	2	11	32	11	12
c	11	12	14	9	5	0	1	1	53	0	51	0	0	2	31	9	13	13
g	9	12	5	6	2	0	0	45	0	4	0	0	0	3	7	5	12	16
t	13	12	25	29	0	53	51	4	0	1	1	0	0	46	4	7	17	12
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc) 0.874 0.680 7.796 0.470 0.935 1.669 0.940 46 68 70 74 53 51 53 59.286 61 
; oligos_7nt_mkv4_m3 versus positions_6nt_m1_rc; m=4/9; ncol2=18; w=14; offset=-1; strand=R; shift=0; score=59.2857; awtgATTGCACAATcmtt
; cor=0.874; Ncor=0.680; logoDP=7.796; NIcor=0.470; NsEucl=0.935; SSD=1.669; NSW=0.940; rcor=46; rNcor=68; rlogoDP=70; rNIcor=74; rNsEucl=53; rSSD=51; rNSW=53; rank_mean=59.286; match_rank=61
a	20	18	4	8	48	0	1	0	0	48	0	55	54	1	13	25	11	12
c	13	11	6	5	1	0	0	0	55	2	52	0	0	4	30	14	13	12
g	9	12	9	36	3	0	0	51	0	3	0	0	0	2	6	7	13	13
t	13	14	36	6	3	55	54	4	0	2	3	0	1	48	6	9	18	18
positions_7nt_m1_rc_shift0 (positions_7nt_m1_rc) 0.867 0.714 3.970 0.107 0.933 1.745 0.938 54 55 95 85 57 54 57 65.286 71 
; oligos_7nt_mkv4_m3 versus positions_7nt_m1_rc; m=5/9; ncol2=17; w=14; offset=-1; strand=R; shift=0; score=65.2857; aaTgATTGCACAATchy-
; cor=0.867; Ncor=0.714; logoDP=3.970; NIcor=0.107; NsEucl=0.933; SSD=1.745; NSW=0.938; rcor=54; rNcor=55; rlogoDP=95; rNIcor=85; rNsEucl=57; rSSD=54; rNSW=57; rank_mean=65.286; match_rank=71
a	24	23	7	9	57	0	1	0	0	66	1	75	75	2	11	19	13	0
c	16	17	6	11	5	0	0	0	75	2	71	0	0	6	43	24	22	0
g	17	18	10	48	8	0	0	69	0	4	0	0	0	1	10	11	17	0
t	18	17	52	7	5	75	74	6	0	3	3	0	0	66	11	21	23	0
oligos_7nt_mkv4_m4_shift3 (oligos_7nt_mkv4_m4) 0.763 0.654 8.787 0.654 0.905 2.584 0.892 93 72 59 42 94 83 93 76.571 84 
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m4; m=6/9; ncol2=12; w=12; offset=2; strand=D; shift=3; score=76.5714; ---krTTGCkCAAyw---
; cor=0.763; Ncor=0.654; logoDP=8.787; NIcor=0.654; NsEucl=0.905; SSD=2.584; NSW=0.892; rcor=93; rNcor=72; rlogoDP=59; rNIcor=42; rNsEucl=94; rSSD=83; rNSW=93; rank_mean=76.571; match_rank=84
a	0	0	0	34	80	0	2	1	0	10	4	168	170	11	61	0	0	0
c	0	0	0	33	28	0	4	0	172	3	165	0	1	53	30	0	0	0
g	0	0	0	44	49	0	0	170	0	58	0	3	1	29	32	0	0	0
t	0	0	0	61	15	172	166	1	0	101	3	1	0	79	49	0	0	0
positions_7nt_m2_rc_shift0 (positions_7nt_m2_rc) 0.779 0.606 8.191 0.587 0.919 2.552 0.909 87 83 68 58 78 78 84 76.571 85 
; oligos_7nt_mkv4_m3 versus positions_7nt_m2_rc; m=7/9; ncol2=18; w=14; offset=-1; strand=R; shift=0; score=76.5714; wyttATTGCGCAATaart
; cor=0.779; Ncor=0.606; logoDP=8.191; NIcor=0.587; NsEucl=0.919; SSD=2.552; NSW=0.909; rcor=87; rNcor=83; rlogoDP=68; rNIcor=58; rNsEucl=78; rSSD=78; rNSW=84; rank_mean=76.571; match_rank=85
a	35	28	19	17	94	0	1	3	4	19	4	113	114	5	57	51	29	28
c	26	32	27	19	10	1	0	0	90	2	108	1	0	6	23	18	25	25
g	25	26	18	23	6	0	1	107	2	90	0	0	1	10	18	27	33	27
t	29	29	51	56	5	114	113	5	19	4	3	1	0	94	17	19	28	35
oligos_7nt_mkv4_m5_rc_shift3 (oligos_7nt_mkv4_m5_rc) 0.771 0.661 6.889 0.550 0.909 2.375 0.901 90 71 72 64 91 75 87 78.571 86 
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m5_rc; m=8/9; ncol2=12; w=12; offset=2; strand=R; shift=3; score=78.5714; ---kaTTrCGCAAyr---
; cor=0.771; Ncor=0.661; logoDP=6.889; NIcor=0.550; NsEucl=0.909; SSD=2.375; NSW=0.901; rcor=90; rNcor=71; rlogoDP=72; rNIcor=64; rNsEucl=91; rSSD=75; rNSW=87; rank_mean=78.571; match_rank=86
a	0	0	0	42	85	3	3	96	2	5	4	168	168	15	46	0	0	0
c	0	0	0	33	28	2	4	2	162	1	150	0	0	43	38	0	0	0
g	0	0	0	45	42	2	13	50	3	165	2	2	2	32	45	0	0	0
t	0	0	0	51	16	164	151	23	4	0	15	1	1	81	42	0	0	0
positions_6nt_m4_shift0 (positions_6nt_m4) 0.771 0.600 8.678 0.579 0.916 2.798 0.900 91 84 62 59 87 89 88 80.000 91 
; oligos_7nt_mkv4_m3 versus positions_6nt_m4; m=9/9; ncol2=18; w=14; offset=-1; strand=D; shift=0; score=     80; mbtgATTGCGCAATcavk
; cor=0.771; Ncor=0.600; logoDP=8.678; NIcor=0.579; NsEucl=0.916; SSD=2.798; NSW=0.900; rcor=91; rNcor=84; rlogoDP=62; rNIcor=59; rNsEucl=87; rSSD=89; rNSW=88; rank_mean=80.000; match_rank=91
a	14	9	6	4	40	0	0	0	3	6	3	46	46	1	5	24	12	9
c	13	13	7	6	3	0	0	0	35	2	43	0	0	2	31	9	12	10
g	10	12	9	31	2	0	0	43	2	35	0	0	0	3	6	7	13	13
t	9	12	24	5	1	46	46	3	6	3	0	0	0	40	4	6	9	14

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift4 ; 11 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv4_m4_shift4 (oligos_7nt_mkv4_m4)                                 
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=12; shift=4; ncol=18; ----krTTGCkCAAyw--
; Alignment reference
a	0	0	0	0	34	80	0	2	1	0	10	4	168	170	11	61	0	0
c	0	0	0	0	33	28	0	4	0	172	3	165	0	1	53	30	0	0
g	0	0	0	0	44	49	0	0	170	0	58	0	3	1	29	32	0	0
t	0	0	0	0	61	15	172	166	1	0	101	3	1	0	79	49	0	0
positions_7nt_m2_shift1 (positions_7nt_m2) 0.909 0.606 10.091 0.600 0.940 1.048 0.956 25 82 47 53 42 22 29 42.857 40 
; oligos_7nt_mkv4_m4 versus positions_7nt_m2; m=1/10; ncol2=18; w=12; offset=-3; strand=D; shift=1; score=42.8571; -ayttATTGCGCAATaar
; cor=0.909; Ncor=0.606; logoDP=10.091; NIcor=0.600; NsEucl=0.940; SSD=1.048; NSW=0.956; rcor=25; rNcor=82; rlogoDP=47; rNIcor=53; rNsEucl=42; rSSD=22; rNSW=29; rank_mean=42.857; match_rank=40
a	0	35	28	19	17	94	0	1	3	4	19	5	113	114	5	56	51	29
c	0	27	33	27	18	10	1	0	0	90	2	107	1	0	6	23	18	26
g	0	25	25	18	23	6	0	1	108	2	90	0	0	1	10	19	27	32
t	0	28	29	51	57	5	114	113	4	19	4	3	1	0	94	17	19	28
oligos_7nt_mkv4_m5_shift4 (oligos_7nt_mkv4_m5) 0.852 0.852 8.701 0.831 0.927 1.533 0.936 61 21 61 15 70 44 59 47.286 47 
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m5; m=2/10; ncol2=12; w=12; offset=0; strand=D; shift=4; score=47.2857; ----yrTTGCGyAAtm--
; cor=0.852; Ncor=0.852; logoDP=8.701; NIcor=0.831; NsEucl=0.927; SSD=1.533; NSW=0.936; rcor=61; rNcor=21; rlogoDP=61; rNIcor=15; rNsEucl=70; rSSD=44; rNSW=59; rank_mean=47.286; match_rank=47
a	0	0	0	0	42	81	1	1	15	0	4	23	151	164	16	51	0	0
c	0	0	0	0	45	32	2	2	2	165	3	50	13	2	42	45	0	0
g	0	0	0	0	38	43	0	0	150	1	162	2	4	2	28	33	0	0
t	0	0	0	0	46	15	168	168	4	5	2	96	3	3	85	42	0	0
positions_7nt_m4_shift1 (positions_7nt_m4) 0.859 0.607 11.728 0.612 0.922 1.740 0.928 58 81 20 48 76 53 65 57.286 58 
; oligos_7nt_mkv4_m4 versus positions_7nt_m4; m=3/10; ncol2=17; w=12; offset=-3; strand=D; shift=1; score=57.2857; -ryTgATTGCACAACtyy
; cor=0.859; Ncor=0.607; logoDP=11.728; NIcor=0.612; NsEucl=0.922; SSD=1.740; NSW=0.928; rcor=58; rNcor=81; rlogoDP=20; rNIcor=48; rNsEucl=76; rSSD=53; rNSW=65; rank_mean=57.286; match_rank=58
a	0	30	15	9	10	58	0	0	0	0	64	0	71	72	1	17	12	15
c	0	11	23	5	9	1	0	0	1	72	2	69	1	0	52	10	24	19
g	0	18	15	7	44	10	0	0	68	0	3	0	0	0	2	9	13	13
t	0	13	19	51	9	3	72	72	3	0	3	3	0	0	17	36	23	25
positions_6nt_m5_shift1 (positions_6nt_m5) 0.849 0.637 11.670 0.643 0.919 1.877 0.922 63 75 22 44 79 62 72 59.571 62 
; oligos_7nt_mkv4_m4 versus positions_6nt_m5; m=4/10; ncol2=16; w=12; offset=-3; strand=D; shift=1; score=59.5714; -aktgATTGCACAACay-
; cor=0.849; Ncor=0.637; logoDP=11.670; NIcor=0.643; NsEucl=0.919; SSD=1.877; NSW=0.922; rcor=63; rNcor=75; rlogoDP=22; rNIcor=44; rNsEucl=79; rSSD=62; rNSW=72; rank_mean=59.571; match_rank=62
a	0	31	15	18	11	69	0	0	2	0	74	0	79	79	1	30	14	0
c	0	15	19	7	10	2	0	0	1	79	1	74	0	0	57	17	28	0
g	0	16	23	9	48	7	0	0	74	0	4	0	0	0	5	13	11	0
t	0	17	22	45	10	1	79	79	2	0	0	5	0	0	16	19	26	0
positions_6nt_m4_shift1 (positions_6nt_m4) 0.865 0.577 10.525 0.567 0.925 1.640 0.932 55 87 40 61 73 50 62 61.143 67 
; oligos_7nt_mkv4_m4 versus positions_6nt_m4; m=5/10; ncol2=18; w=12; offset=-3; strand=D; shift=1; score=61.1429; -mbtgATTGCGCAATcav
; cor=0.865; Ncor=0.577; logoDP=10.525; NIcor=0.567; NsEucl=0.925; SSD=1.640; NSW=0.932; rcor=55; rNcor=87; rlogoDP=40; rNIcor=61; rNsEucl=73; rSSD=50; rNSW=62; rank_mean=61.143; match_rank=67
a	0	14	9	6	4	40	0	0	0	3	6	3	46	46	1	5	24	12
c	0	13	13	7	6	3	0	0	0	35	2	43	0	0	2	31	9	12
g	0	10	12	9	31	2	0	0	43	2	35	0	0	0	3	6	7	13
t	0	9	12	24	5	1	46	46	3	6	3	0	0	0	40	4	6	9
positions_6nt_m2_shift1 (positions_6nt_m2) 0.830 0.554 11.343 0.559 0.914 2.145 0.911 72 93 25 62 90 72 83 71.000 76 
; oligos_7nt_mkv4_m4 versus positions_6nt_m2; m=6/10; ncol2=18; w=12; offset=-3; strand=D; shift=1; score=     71; -mwgTGTTGCACAATcac
; cor=0.830; Ncor=0.554; logoDP=11.343; NIcor=0.559; NsEucl=0.914; SSD=2.145; NSW=0.911; rcor=72; rNcor=93; rlogoDP=25; rNIcor=62; rNsEucl=90; rSSD=72; rNSW=83; rank_mean=71.000; match_rank=76
a	0	12	13	6	4	5	0	0	2	0	37	1	41	41	0	5	26	9
c	0	14	1	7	2	4	0	0	0	42	1	40	0	0	1	24	6	16
g	0	7	8	27	5	31	0	0	39	0	3	0	0	1	3	9	3	9
t	0	9	20	2	31	2	42	42	1	0	1	1	1	0	38	4	7	8
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc) 0.846 0.564 9.529 0.474 0.918 1.923 0.920 67 90 58 72 82 65 74 72.571 78 
; oligos_7nt_mkv4_m4 versus positions_6nt_m3_rc; m=7/10; ncol2=18; w=12; offset=-3; strand=R; shift=1; score=72.5714; -aaytATTGCACAATcat
; cor=0.846; Ncor=0.564; logoDP=9.529; NIcor=0.474; NsEucl=0.918; SSD=1.923; NSW=0.920; rcor=67; rNcor=90; rlogoDP=58; rNIcor=72; rNsEucl=82; rSSD=65; rNSW=74; rank_mean=72.571; match_rank=78
a	0	20	17	9	9	46	0	1	3	0	48	1	53	53	2	11	32	11
c	0	11	12	14	9	5	0	1	1	53	0	51	0	0	2	31	9	13
g	0	9	12	5	6	2	0	0	45	0	4	0	0	0	3	7	5	12
t	0	13	12	25	29	0	53	51	4	0	1	1	0	0	46	4	7	17
positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc) 0.845 0.564 9.817 0.472 0.917 1.968 0.918 68 91 54 73 85 67 77 73.571 80 
; oligos_7nt_mkv4_m4 versus positions_6nt_m1_rc; m=8/10; ncol2=18; w=12; offset=-3; strand=R; shift=1; score=73.5714; -awtgATTGCACAATcmt
; cor=0.845; Ncor=0.564; logoDP=9.817; NIcor=0.472; NsEucl=0.917; SSD=1.968; NSW=0.918; rcor=68; rNcor=91; rlogoDP=54; rNIcor=73; rNsEucl=85; rSSD=67; rNSW=77; rank_mean=73.571; match_rank=80
a	0	20	18	4	8	48	0	1	0	0	48	0	55	54	1	13	25	11
c	0	13	11	6	5	1	0	0	0	55	2	52	0	0	4	30	14	13
g	0	9	12	9	36	3	0	0	51	0	3	0	0	0	2	6	7	13
t	0	13	14	36	6	3	55	54	4	0	2	3	0	1	48	6	9	18
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc) 0.849 0.599 3.836 0.044 0.919 1.900 0.921 65 85 97 94 80 64 73 79.714 90 
; oligos_7nt_mkv4_m4 versus positions_7nt_m1_rc; m=9/10; ncol2=17; w=12; offset=-3; strand=R; shift=1; score=79.7143; -aaTgATTGCACAATchy
; cor=0.849; Ncor=0.599; logoDP=3.836; NIcor=0.044; NsEucl=0.919; SSD=1.900; NSW=0.921; rcor=65; rNcor=85; rlogoDP=97; rNIcor=94; rNsEucl=80; rSSD=64; rNSW=73; rank_mean=79.714; match_rank=90
a	0	24	23	7	9	57	0	1	0	0	66	1	75	75	2	11	19	13
c	0	16	17	6	11	5	0	0	0	75	2	71	0	0	6	43	24	22
g	0	17	18	10	48	8	0	0	69	0	4	0	0	0	1	10	11	17
t	0	18	17	52	7	5	75	74	6	0	3	3	0	0	66	11	21	23
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc) 0.835 0.557 4.751 0.198 0.914 2.118 0.912 70 92 83 84 89 70 82 81.429 94 
; oligos_7nt_mkv4_m4 versus positions_7nt_m5_rc; m=10/10; ncol2=18; w=12; offset=-4; strand=R; shift=0; score=81.4286; ymdgTGTTGCACAATcwc
; cor=0.835; Ncor=0.557; logoDP=4.751; NIcor=0.198; NsEucl=0.914; SSD=2.118; NSW=0.912; rcor=70; rNcor=92; rlogoDP=83; rNIcor=84; rNsEucl=89; rSSD=70; rNSW=82; rank_mean=81.429; match_rank=94
a	10	19	14	10	3	6	0	0	2	0	46	0	54	54	1	5	19	9
c	15	17	3	10	2	5	0	0	1	54	2	53	0	0	1	29	10	21
g	11	6	15	29	7	41	0	1	50	0	3	0	0	0	3	12	7	13
t	18	12	22	5	42	2	54	53	1	0	3	1	0	0	49	8	18	11

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift3 ; 6 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5)                                 
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=12; shift=3; ncol=18; ---yrTTGCGyAAtm---
; Alignment reference
a	0	0	0	42	81	1	1	15	0	4	23	151	164	16	51	0	0	0
c	0	0	0	45	32	2	2	2	165	3	50	13	2	42	45	0	0	0
g	0	0	0	38	43	0	0	150	1	162	2	4	2	28	33	0	0	0
t	0	0	0	46	15	168	168	4	5	2	96	3	3	85	42	0	0	0
positions_7nt_m2_shift0 (positions_7nt_m2) 0.887 0.591 8.115 0.576 0.934 1.269 0.947 37 86 69 60 55 28 44 54.143 55 
; oligos_7nt_mkv4_m5 versus positions_7nt_m2; m=1/5; ncol2=18; w=12; offset=-3; strand=D; shift=0; score=54.1429; ayttATTGCGCAATaarw
; cor=0.887; Ncor=0.591; logoDP=8.115; NIcor=0.576; NsEucl=0.934; SSD=1.269; NSW=0.947; rcor=37; rNcor=86; rlogoDP=69; rNIcor=60; rNsEucl=55; rSSD=28; rNSW=44; rank_mean=54.143; match_rank=55
a	35	28	19	17	94	0	1	3	4	19	5	113	114	5	56	51	29	29
c	27	33	27	18	10	1	0	0	90	2	107	1	0	6	23	18	26	25
g	25	25	18	23	6	0	1	108	2	90	0	0	1	10	19	27	32	26
t	28	29	51	57	5	114	113	4	19	4	3	1	0	94	17	19	28	35
positions_6nt_m4_shift0 (positions_6nt_m4) 0.850 0.567 8.335 0.550 0.921 1.796 0.925 62 89 67 65 77 57 68 69.286 73 
; oligos_7nt_mkv4_m5 versus positions_6nt_m4; m=2/5; ncol2=18; w=12; offset=-3; strand=D; shift=0; score=69.2857; mbtgATTGCGCAATcavk
; cor=0.850; Ncor=0.567; logoDP=8.335; NIcor=0.550; NsEucl=0.921; SSD=1.796; NSW=0.925; rcor=62; rNcor=89; rlogoDP=67; rNIcor=65; rNsEucl=77; rSSD=57; rNSW=68; rank_mean=69.286; match_rank=73
a	14	9	6	4	40	0	0	0	3	6	3	46	46	1	5	24	12	9
c	13	13	7	6	3	0	0	0	35	2	43	0	0	2	31	9	12	10
g	10	12	9	31	2	0	0	43	2	35	0	0	0	3	6	7	13	13
t	9	12	24	5	1	46	46	3	6	3	0	0	0	40	4	6	9	14
positions_6nt_m3_shift0 (positions_6nt_m3) 0.764 0.509 8.758 0.493 0.901 2.846 0.881 92 96 60 69 96 92 96 85.857 96 
; oligos_7nt_mkv4_m5 versus positions_6nt_m3; m=3/5; ncol2=18; w=12; offset=-3; strand=D; shift=0; score=85.8571; catgATTGTGCAATartt
; cor=0.764; Ncor=0.509; logoDP=8.758; NIcor=0.493; NsEucl=0.901; SSD=2.846; NSW=0.881; rcor=92; rNcor=96; rlogoDP=60; rNIcor=69; rNsEucl=96; rSSD=92; rNSW=96; rank_mean=85.857; match_rank=96
a	12	17	7	4	46	0	0	1	1	0	4	51	53	0	29	25	12	13
c	16	12	5	7	3	0	0	0	4	0	45	0	0	2	6	5	12	9
g	13	13	9	31	2	0	0	51	0	53	1	1	0	5	9	14	12	11
t	12	11	32	11	2	53	53	1	48	0	3	1	0	46	9	9	17	20
positions_6nt_m1_rc_shift0 (positions_6nt_m1_rc) 0.751 0.501 8.666 0.487 0.897 3.040 0.873 97 98 63 70 98 95 98 88.429 97 
; oligos_7nt_mkv4_m5 versus positions_6nt_m1_rc; m=4/5; ncol2=18; w=12; offset=-3; strand=R; shift=0; score=88.4286; awtgATTGCACAATcmtt
; cor=0.751; Ncor=0.501; logoDP=8.666; NIcor=0.487; NsEucl=0.897; SSD=3.040; NSW=0.873; rcor=97; rNcor=98; rlogoDP=63; rNIcor=70; rNsEucl=98; rSSD=95; rNSW=98; rank_mean=88.429; match_rank=97
a	20	18	4	8	48	0	1	0	0	48	0	55	54	1	13	25	11	12
c	13	11	6	5	1	0	0	0	55	2	52	0	0	4	30	14	13	12
g	9	12	9	36	3	0	0	51	0	3	0	0	0	2	6	7	13	13
t	13	14	36	6	3	55	54	4	0	2	3	0	1	48	6	9	18	18
positions_7nt_m1_rc_shift0 (positions_7nt_m1_rc) 0.753 0.532 3.133 0.034 0.898 2.973 0.876 96 94 98 96 97 94 97 96.000 98 
; oligos_7nt_mkv4_m5 versus positions_7nt_m1_rc; m=5/5; ncol2=17; w=12; offset=-3; strand=R; shift=0; score=     96; aaTgATTGCACAATchy-
; cor=0.753; Ncor=0.532; logoDP=3.133; NIcor=0.034; NsEucl=0.898; SSD=2.973; NSW=0.876; rcor=96; rNcor=94; rlogoDP=98; rNIcor=96; rNsEucl=97; rSSD=94; rNSW=97; rank_mean=96.000; match_rank=98
a	24	23	7	9	57	0	1	0	0	66	1	75	75	2	11	19	13	0
c	16	17	6	11	5	0	0	0	75	2	71	0	0	6	43	24	22	0
g	17	18	10	48	8	0	0	69	0	4	0	0	0	1	10	11	17	0
t	18	17	52	7	5	75	74	6	0	3	3	0	0	66	11	21	23	0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift1 ; 4 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_mkv3_m3_shift1 (oligos_6nt_mkv3_m3)                                 
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=1; ncol=18; -dhGATTGCGhm------
; Alignment reference
a	0	20	21	2	60	0	5	6	0	0	21	38	0	0	0	0	0	0
c	0	8	17	1	2	1	2	1	65	2	18	18	0	0	0	0	0	0
g	0	20	12	54	4	1	0	59	0	62	3	5	0	0	0	0	0	0
t	0	19	17	10	1	65	60	1	2	3	25	6	0	0	0	0	0	0
oligos_7nt_mkv4_m5_shift3 (oligos_7nt_mkv4_m5) 0.888 0.571 6.020 0.555 0.924 0.937 0.948 35 88 74 63 74 19 43 56.571 57 
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m5; m=1/3; ncol2=12; w=9; offset=2; strand=D; shift=3; score=56.5714; ---yrTTGCGyAAtm---
; cor=0.888; Ncor=0.571; logoDP=6.020; NIcor=0.555; NsEucl=0.924; SSD=0.937; NSW=0.948; rcor=35; rNcor=88; rlogoDP=74; rNIcor=63; rNsEucl=74; rSSD=19; rNSW=43; rank_mean=56.571; match_rank=57
a	0	0	0	42	81	1	1	15	0	4	23	151	164	16	51	0	0	0
c	0	0	0	45	32	2	2	2	165	3	50	13	2	42	45	0	0	0
g	0	0	0	38	43	0	0	150	1	162	2	4	2	28	33	0	0	0
t	0	0	0	46	15	168	168	4	5	2	96	3	3	85	42	0	0	0
positions_6nt_m4_shift0 (positions_6nt_m4) 0.870 0.531 5.881 0.512 0.928 1.250 0.943 51 95 76 66 67 27 48 61.429 68 
; oligos_6nt_mkv3_m3 versus positions_6nt_m4; m=2/3; ncol2=18; w=11; offset=-1; strand=D; shift=0; score=61.4286; mbtgATTGCGCAATcavk
; cor=0.870; Ncor=0.531; logoDP=5.881; NIcor=0.512; NsEucl=0.928; SSD=1.250; NSW=0.943; rcor=51; rNcor=95; rlogoDP=76; rNIcor=66; rNsEucl=67; rSSD=27; rNSW=48; rank_mean=61.429; match_rank=68
a	14	9	6	4	40	0	0	0	3	6	3	46	46	1	5	24	12	9
c	13	13	7	6	3	0	0	0	35	2	43	0	0	2	31	9	12	10
g	10	12	9	31	2	0	0	43	2	35	0	0	0	3	6	7	13	13
t	9	12	24	5	1	46	46	3	6	3	0	0	0	40	4	6	9	14
positions_7nt_m2_shift0 (positions_7nt_m2) 0.821 0.501 5.595 0.480 0.918 1.639 0.925 77 97 77 71 84 49 67 74.571 81 
; oligos_6nt_mkv3_m3 versus positions_7nt_m2; m=3/3; ncol2=18; w=11; offset=-1; strand=D; shift=0; score=74.5714; ayttATTGCGCAATaarw
; cor=0.821; Ncor=0.501; logoDP=5.595; NIcor=0.480; NsEucl=0.918; SSD=1.639; NSW=0.925; rcor=77; rNcor=97; rlogoDP=77; rNIcor=71; rNsEucl=84; rSSD=49; rNSW=67; rank_mean=74.571; match_rank=81
a	35	28	19	17	94	0	1	3	4	19	5	113	114	5	56	51	29	29
c	27	33	27	18	10	1	0	0	90	2	107	1	0	6	23	18	26	25
g	25	25	18	23	6	0	1	108	2	90	0	0	1	10	19	27	32	26
t	28	29	51	57	5	114	113	4	19	4	3	1	0	94	17	19	28	35

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift1 ; 3 matrices ; sort_field=rank_mean

Matrix nameAligned logoscor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
positions_7nt_m2_shift1 (positions_7nt_m2)                                 
; positions_7nt_m2; m=0 (reference); ncol1=18; shift=1; ncol=19; -ayttATTGCGCAATaarw
; Alignment reference
a	0	35	28	19	17	94	0	1	3	4	19	5	113	114	5	56	51	29	29
c	0	27	33	27	18	10	1	0	0	90	2	107	1	0	6	23	18	26	25
g	0	25	25	18	23	6	0	1	108	2	90	0	0	1	10	19	27	32	26
t	0	28	29	51	57	5	114	113	4	19	4	3	1	0	94	17	19	28	35
positions_7nt_m4_shift1 (positions_7nt_m4) 0.791 0.747 10.760 0.751 0.931 2.745 0.919 82 46 36 29 62 88 76 59.857 63 
; positions_7nt_m2 versus positions_7nt_m4; m=1/2; ncol2=17; w=17; offset=0; strand=D; shift=1; score=59.8571; -ryTgATTGCACAACtyy-
; cor=0.791; Ncor=0.747; logoDP=10.760; NIcor=0.751; NsEucl=0.931; SSD=2.745; NSW=0.919; rcor=82; rNcor=46; rlogoDP=36; rNIcor=29; rNsEucl=62; rSSD=88; rNSW=76; rank_mean=59.857; match_rank=63
a	0	30	15	9	10	58	0	0	0	0	64	0	71	72	1	17	12	15	0
c	0	11	23	5	9	1	0	0	1	72	2	69	1	0	52	10	24	19	0
g	0	18	15	7	44	10	0	0	68	0	3	0	0	0	2	9	13	13	0
t	0	13	19	51	9	3	72	72	3	0	3	3	0	0	17	36	23	25	0
positions_7nt_m5_rc_shift0 (positions_7nt_m5_rc) 0.782 0.700 3.973 0.217 0.929 2.931 0.914 86 62 94 83 66 93 81 80.714 93 
; positions_7nt_m2 versus positions_7nt_m5_rc; m=2/2; ncol2=18; w=17; offset=-1; strand=R; shift=0; score=80.7143; ymdgTGTTGCACAATcwc-
; cor=0.782; Ncor=0.700; logoDP=3.973; NIcor=0.217; NsEucl=0.929; SSD=2.931; NSW=0.914; rcor=86; rNcor=62; rlogoDP=94; rNIcor=83; rNsEucl=66; rSSD=93; rNSW=81; rank_mean=80.714; match_rank=93
a	10	19	14	10	3	6	0	0	2	0	46	0	54	54	1	5	19	9	0
c	15	17	3	10	2	5	0	0	1	54	2	53	0	0	1	29	10	21	0
g	11	6	15	29	7	41	0	1	50	0	3	0	0	0	3	12	7	13	0
t	18	12	22	5	42	2	54	53	1	0	3	1	0	0	49	8	18	11	0