One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m3_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
dyads_test_vs_ctrl_m3_shift0 (dyads_test_vs_ctrl_m3)
; dyads_test_vs_ctrl_m3; m=0 (reference); ncol1=28; shift=0; ncol=29; wwGATawwawwwTAGrwwmwwwwAAAww- ; Alignment reference a 49 73 12 131 5 69 66 51 52 65 52 63 12 121 14 74 57 52 63 69 52 93 83 129 117 113 66 49 0 c 19 16 7 3 4 20 0 31 33 22 31 28 7 4 4 3 22 26 46 0 21 1 2 8 12 13 14 33 0 g 34 16 115 4 3 23 33 28 27 22 27 4 10 8 119 44 2 1 36 22 35 2 6 4 5 5 25 24 0 t 47 44 15 11 137 37 50 39 37 40 39 54 120 16 12 28 68 70 4 58 41 53 58 8 15 18 44 43 0

dyads_test_vs_ctrl_m5_shift0 (dyads_test_vs_ctrl_m5) 0.931 0.899 4.038 0.877 0.977 0.804 0.986 1 1 6 1 1 1 1 1.714 1
; dyads_test_vs_ctrl_m3 versus dyads_test_vs_ctrl_m5; m=1/1; ncol2=29; w=28; offset=0; strand=D; shift=0; score= 1.7143; awGATaawwwamTAGrwwmwwwwwAAAww ; cor=0.931; Ncor=0.899; logoDP=4.038; NIcor=0.877; NsEucl=0.977; SSD=0.804; NSW=0.986; rcor=1; rNcor=1; rlogoDP=6; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.714; match_rank=1 a 58 70 12 130 4 60 71 58 45 65 54 90 21 118 19 69 50 45 56 65 53 90 96 73 118 115 133 47 55 c 21 11 5 2 5 18 20 23 29 17 27 37 8 1 2 5 20 30 48 1 21 1 2 26 10 11 2 24 29 g 33 17 114 6 2 34 20 26 29 20 29 8 9 11 106 44 1 3 33 29 33 3 1 4 2 7 3 23 18 t 32 46 13 6 133 32 33 37 41 42 34 9 106 14 17 26 73 66 7 49 37 50 45 41 14 11 6 50 42

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m3_shift0 (dyads_test_vs_ctrl_m3)																		; dyads_test_vs_ctrl_m3; m=0 (reference); ncol1=28; shift=0; ncol=29; wwGATawwawwwTAGrwwmwwwwAAAww- ; Alignment reference a 49 73 12 131 5 69 66 51 52 65 52 63 12 121 14 74 57 52 63 69 52 93 83 129 117 113 66 49 0 c 19 16 7 3 4 20 0 31 33 22 31 28 7 4 4 3 22 26 46 0 21 1 2 8 12 13 14 33 0 g 34 16 115 4 3 23 33 28 27 22 27 4 10 8 119 44 2 1 36 22 35 2 6 4 5 5 25 24 0 t 47 44 15 11 137 37 50 39 37 40 39 54 120 16 12 28 68 70 4 58 41 53 58 8 15 18 44 43 0
dyads_test_vs_ctrl_m5_shift0 (dyads_test_vs_ctrl_m5)		0.931	0.899	4.038	0.877	0.977	0.804	0.986	1	1	6	1	1	1	1	1.714	1	; dyads_test_vs_ctrl_m3 versus dyads_test_vs_ctrl_m5; m=1/1; ncol2=29; w=28; offset=0; strand=D; shift=0; score= 1.7143; awGATaawwwamTAGrwwmwwwwwAAAww ; cor=0.931; Ncor=0.899; logoDP=4.038; NIcor=0.877; NsEucl=0.977; SSD=0.804; NSW=0.986; rcor=1; rNcor=1; rlogoDP=6; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.714; match_rank=1 a 58 70 12 130 4 60 71 58 45 65 54 90 21 118 19 69 50 45 56 65 53 90 96 73 118 115 133 47 55 c 21 11 5 2 5 18 20 23 29 17 27 37 8 1 2 5 20 30 48 1 21 1 2 26 10 11 2 24 29 g 33 17 114 6 2 34 20 26 29 20 29 8 9 11 106 44 1 3 33 29 33 3 1 4 2 7 3 23 18 t 32 46 13 6 133 32 33 37 41 42 34 9 106 14 17 26 73 66 7 49 37 50 45 41 14 11 6 50 42

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift8 ; 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_6nt_test_vs_ctrl_m1_shift8 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=8; ncol=32; --------aaTgAGATAAAaAttaaAaTcTww ; Alignment reference a 0 0 0 0 0 0 0 0 44 41 8 20 101 16 108 7 99 112 97 82 83 24 23 80 81 90 80 16 21 16 40 45 c 0 0 0 0 0 0 0 0 24 29 1 12 3 12 2 3 6 0 4 13 6 19 16 7 17 7 13 2 67 7 19 25 g 0 0 0 0 0 0 0 0 25 22 8 77 6 86 5 4 8 3 8 9 9 11 16 12 6 8 9 11 10 3 25 13 t 0 0 0 0 0 0 0 0 28 29 104 12 11 7 6 107 8 6 12 17 23 67 66 22 17 16 19 92 23 95 37 38

oligos_6nt_test_vs_ctrl_m5_shift8 (oligos_6nt_test_vs_ctrl_m5) 0.859 0.859 4.769 0.853 0.959 1.891 0.961 5 2 2 2 4 8 6 4.143 2
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=1/4; ncol2=24; w=24; offset=0; strand=D; shift=8; score= 4.1429; --------wwcAAGATAAAaattaaaATcTww ; cor=0.859; Ncor=0.859; logoDP=4.769; NIcor=0.853; NsEucl=0.959; SSD=1.891; NSW=0.961; rcor=5; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=4; rSSD=8; rNSW=6; rank_mean=4.143; match_rank=2 a 0 0 0 0 0 0 0 0 58 55 30 138 138 17 136 7 131 136 118 97 98 25 37 94 101 91 109 20 35 33 44 67 c 0 0 0 0 0 0 0 0 26 28 78 5 4 9 4 7 4 2 10 13 15 13 16 10 15 14 11 12 75 8 26 25 g 0 0 0 0 0 0 0 0 28 22 18 2 1 110 6 5 7 4 8 12 16 11 14 19 10 14 10 11 18 6 29 18 t 0 0 0 0 0 0 0 0 38 45 24 5 7 14 4 131 8 8 14 28 21 101 83 27 24 31 20 107 22 103 51 40

oligos_6nt_test_vs_ctrl_m2_shift7 (oligos_6nt_test_vs_ctrl_m2) 0.853 0.784 4.594 0.770 0.957 1.926 0.958 6 3 3 3 5 10 8 5.429 4
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=2/4; ncol2=24; w=23; offset=-1; strand=D; shift=7; score= 5.4286; -------watAgAGATAAAaAttaaaawhww- ; cor=0.853; Ncor=0.784; logoDP=4.594; NIcor=0.770; NsEucl=0.957; SSD=1.926; NSW=0.958; rcor=6; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=5; rSSD=10; rNSW=8; rank_mean=5.429; match_rank=4 a 0 0 0 0 0 0 0 58 80 42 181 36 194 26 197 12 184 187 162 138 151 50 43 140 134 139 139 53 64 80 73 0 c 0 0 0 0 0 0 0 43 40 32 1 13 3 6 6 6 6 7 18 19 11 11 26 16 18 21 17 18 55 40 42 0 g 0 0 0 0 0 0 0 40 43 32 14 144 4 167 5 6 10 8 9 21 24 16 19 23 20 18 24 22 38 28 35 0 t 0 0 0 0 0 0 0 71 49 106 16 19 11 13 4 188 12 10 23 34 26 135 124 33 40 34 32 119 55 64 62 0

oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3) 0.829 0.414 3.658 0.413 0.942 1.743 0.946 9 14 10 10 11 6 11 10.143 10
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=3/4; ncol2=24; w=16; offset=-8; strand=D; shift=0; score=10.1429; wwaaTtTTTATCAGATAAAwAwww-------- ; cor=0.829; Ncor=0.414; logoDP=3.658; NIcor=0.413; NsEucl=0.942; SSD=1.743; NSW=0.946; rcor=9; rNcor=14; rlogoDP=10; rNIcor=10; rNsEucl=11; rSSD=6; rNSW=11; rank_mean=10.143; match_rank=10 a 43 51 73 75 17 31 18 9 17 104 6 14 114 13 107 6 113 101 91 73 88 33 48 42 0 0 0 0 0 0 0 0 c 20 21 17 12 13 10 8 5 6 5 12 87 2 7 9 6 4 6 12 14 8 10 21 20 0 0 0 0 0 0 0 0 g 18 18 16 20 5 13 10 12 8 7 11 5 2 98 4 4 3 6 8 8 13 7 20 24 0 0 0 0 0 0 0 0 t 47 38 22 21 93 74 92 102 97 12 99 22 10 10 8 112 8 15 17 33 19 78 39 42 0 0 0 0 0 0 0 0

oligos_7nt_test_vs_ctrl_m1_rc_shift6 (oligos_7nt_test_vs_ctrl_m1_rc) 0.767 0.413 2.680 0.184 0.923 2.309 0.918 15 15 11 11 15 13 16 13.714 16
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1_rc; m=4/4; ncol2=16; w=14; offset=-2; strand=R; shift=6; score=13.7143; ------wwTATCAGATAAAgww---------- ; cor=0.767; Ncor=0.413; logoDP=2.680; NIcor=0.184; NsEucl=0.923; SSD=2.309; NSW=0.918; rcor=15; rNcor=15; rlogoDP=11; rNIcor=11; rNsEucl=15; rSSD=13; rNSW=16; rank_mean=13.714; match_rank=16 a 0 0 0 0 0 0 123 158 51 392 26 37 407 34 407 15 394 353 351 76 153 161 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 78 69 35 18 16 357 2 19 16 18 14 29 31 44 72 89 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 105 75 40 16 29 25 6 379 15 14 16 29 28 230 94 69 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 146 150 326 26 381 33 37 20 14 405 28 41 42 102 133 133 0 0 0 0 0 0 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
oligos_6nt_test_vs_ctrl_m1_shift8 (oligos_6nt_test_vs_ctrl_m1)																	; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=8; ncol=32; --------aaTgAGATAAAaAttaaAaTcTww ; Alignment reference a 0 0 0 0 0 0 0 0 44 41 8 20 101 16 108 7 99 112 97 82 83 24 23 80 81 90 80 16 21 16 40 45 c 0 0 0 0 0 0 0 0 24 29 1 12 3 12 2 3 6 0 4 13 6 19 16 7 17 7 13 2 67 7 19 25 g 0 0 0 0 0 0 0 0 25 22 8 77 6 86 5 4 8 3 8 9 9 11 16 12 6 8 9 11 10 3 25 13 t 0 0 0 0 0 0 0 0 28 29 104 12 11 7 6 107 8 6 12 17 23 67 66 22 17 16 19 92 23 95 37 38
oligos_6nt_test_vs_ctrl_m5_shift8 (oligos_6nt_test_vs_ctrl_m5)	0.859	0.859	4.769	0.853	0.959	1.891	0.961	5	2	2	2	4	8	6	4.143	2	; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=1/4; ncol2=24; w=24; offset=0; strand=D; shift=8; score= 4.1429; --------wwcAAGATAAAaattaaaATcTww ; cor=0.859; Ncor=0.859; logoDP=4.769; NIcor=0.853; NsEucl=0.959; SSD=1.891; NSW=0.961; rcor=5; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=4; rSSD=8; rNSW=6; rank_mean=4.143; match_rank=2 a 0 0 0 0 0 0 0 0 58 55 30 138 138 17 136 7 131 136 118 97 98 25 37 94 101 91 109 20 35 33 44 67 c 0 0 0 0 0 0 0 0 26 28 78 5 4 9 4 7 4 2 10 13 15 13 16 10 15 14 11 12 75 8 26 25 g 0 0 0 0 0 0 0 0 28 22 18 2 1 110 6 5 7 4 8 12 16 11 14 19 10 14 10 11 18 6 29 18 t 0 0 0 0 0 0 0 0 38 45 24 5 7 14 4 131 8 8 14 28 21 101 83 27 24 31 20 107 22 103 51 40
oligos_6nt_test_vs_ctrl_m2_shift7 (oligos_6nt_test_vs_ctrl_m2)	0.853	0.784	4.594	0.770	0.957	1.926	0.958	6	3	3	3	5	10	8	5.429	4	; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=2/4; ncol2=24; w=23; offset=-1; strand=D; shift=7; score= 5.4286; -------watAgAGATAAAaAttaaaawhww- ; cor=0.853; Ncor=0.784; logoDP=4.594; NIcor=0.770; NsEucl=0.957; SSD=1.926; NSW=0.958; rcor=6; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=5; rSSD=10; rNSW=8; rank_mean=5.429; match_rank=4 a 0 0 0 0 0 0 0 58 80 42 181 36 194 26 197 12 184 187 162 138 151 50 43 140 134 139 139 53 64 80 73 0 c 0 0 0 0 0 0 0 43 40 32 1 13 3 6 6 6 6 7 18 19 11 11 26 16 18 21 17 18 55 40 42 0 g 0 0 0 0 0 0 0 40 43 32 14 144 4 167 5 6 10 8 9 21 24 16 19 23 20 18 24 22 38 28 35 0 t 0 0 0 0 0 0 0 71 49 106 16 19 11 13 4 188 12 10 23 34 26 135 124 33 40 34 32 119 55 64 62 0
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)	0.829	0.414	3.658	0.413	0.942	1.743	0.946	9	14	10	10	11	6	11	10.143	10	; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m3; m=3/4; ncol2=24; w=16; offset=-8; strand=D; shift=0; score=10.1429; wwaaTtTTTATCAGATAAAwAwww-------- ; cor=0.829; Ncor=0.414; logoDP=3.658; NIcor=0.413; NsEucl=0.942; SSD=1.743; NSW=0.946; rcor=9; rNcor=14; rlogoDP=10; rNIcor=10; rNsEucl=11; rSSD=6; rNSW=11; rank_mean=10.143; match_rank=10 a 43 51 73 75 17 31 18 9 17 104 6 14 114 13 107 6 113 101 91 73 88 33 48 42 0 0 0 0 0 0 0 0 c 20 21 17 12 13 10 8 5 6 5 12 87 2 7 9 6 4 6 12 14 8 10 21 20 0 0 0 0 0 0 0 0 g 18 18 16 20 5 13 10 12 8 7 11 5 2 98 4 4 3 6 8 8 13 7 20 24 0 0 0 0 0 0 0 0 t 47 38 22 21 93 74 92 102 97 12 99 22 10 10 8 112 8 15 17 33 19 78 39 42 0 0 0 0 0 0 0 0
oligos_7nt_test_vs_ctrl_m1_rc_shift6 (oligos_7nt_test_vs_ctrl_m1_rc)	0.767	0.413	2.680	0.184	0.923	2.309	0.918	15	15	11	11	15	13	16	13.714	16	; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1_rc; m=4/4; ncol2=16; w=14; offset=-2; strand=R; shift=6; score=13.7143; ------wwTATCAGATAAAgww---------- ; cor=0.767; Ncor=0.413; logoDP=2.680; NIcor=0.184; NsEucl=0.923; SSD=2.309; NSW=0.918; rcor=15; rNcor=15; rlogoDP=11; rNIcor=11; rNsEucl=15; rSSD=13; rNSW=16; rank_mean=13.714; match_rank=16 a 0 0 0 0 0 0 123 158 51 392 26 37 407 34 407 15 394 353 351 76 153 161 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 78 69 35 18 16 357 2 19 16 18 14 29 31 44 72 89 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 105 75 40 16 29 25 6 379 15 14 16 29 28 230 94 69 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 146 150 326 26 381 33 37 20 14 405 28 41 42 102 133 133 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_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
dyads_test_vs_ctrl_m2_shift0 (dyads_test_vs_ctrl_m2)
; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=26; shift=0; ncol=29; wwGATwwwwwwwwwkawhmwwAAAww--- ; Alignment reference a 117 148 14 318 9 113 157 104 112 116 115 153 147 192 16 159 128 117 141 156 130 318 307 319 113 120 0 0 0 c 56 26 19 7 4 73 2 68 68 55 59 80 8 3 58 48 50 94 113 6 67 6 16 5 59 63 0 0 0 g 69 69 282 8 4 67 63 62 50 55 59 5 9 6 157 76 2 5 73 69 5 7 11 8 59 62 0 0 0 t 101 100 28 10 326 90 121 109 113 117 110 105 179 142 112 60 163 127 16 112 141 12 9 11 112 98 0 0 0

dyads_test_vs_ctrl_m3_shift0 (dyads_test_vs_ctrl_m3) 0.837 0.777 4.096 0.742 0.964 1.737 0.967 7 4 4 5 2 5 3 4.286 3
; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m3; m=1/2; ncol2=28; w=26; offset=0; strand=D; shift=0; score= 4.2857; wwGATawwawwwTAGrwwmwwwwAAAww- ; cor=0.837; Ncor=0.777; logoDP=4.096; NIcor=0.742; NsEucl=0.964; SSD=1.737; NSW=0.967; rcor=7; rNcor=4; rlogoDP=4; rNIcor=5; rNsEucl=2; rSSD=5; rNSW=3; rank_mean=4.286; match_rank=3 a 49 73 12 131 5 69 66 51 52 65 52 63 12 121 14 74 57 52 63 69 52 93 83 129 117 113 66 49 0 c 19 16 7 3 4 20 0 31 33 22 31 28 7 4 4 3 22 26 46 0 21 1 2 8 12 13 14 33 0 g 34 16 115 4 3 23 33 28 27 22 27 4 10 8 119 44 2 1 36 22 35 2 6 4 5 5 25 24 0 t 47 44 15 11 137 37 50 39 37 40 39 54 120 16 12 28 68 70 4 58 41 53 58 8 15 18 44 43 0

dyads_test_vs_ctrl_m5_shift0 (dyads_test_vs_ctrl_m5) 0.810 0.726 3.714 0.685 0.962 1.978 0.962 10 6 9 6 3 11 4 7.000 6
; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m5; m=2/2; ncol2=29; w=26; offset=0; strand=D; shift=0; score= 7; awGATaawwwamTAGrwwmwwwwwAAAww ; cor=0.810; Ncor=0.726; logoDP=3.714; NIcor=0.685; NsEucl=0.962; SSD=1.978; NSW=0.962; rcor=10; rNcor=6; rlogoDP=9; rNIcor=6; rNsEucl=3; rSSD=11; rNSW=4; rank_mean=7.000; match_rank=6 a 58 70 12 130 4 60 71 58 45 65 54 90 21 118 19 69 50 45 56 65 53 90 96 73 118 115 133 47 55 c 21 11 5 2 5 18 20 23 29 17 27 37 8 1 2 5 20 30 48 1 21 1 2 26 10 11 2 24 29 g 33 17 114 6 2 34 20 26 29 20 29 8 9 11 106 44 1 3 33 29 33 3 1 4 2 7 3 23 18 t 32 46 13 6 133 32 33 37 41 42 34 9 106 14 17 26 73 66 7 49 37 50 45 41 14 11 6 50 42

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m2_shift0 (dyads_test_vs_ctrl_m2)																	; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=26; shift=0; ncol=29; wwGATwwwwwwwwwkawhmwwAAAww--- ; Alignment reference a 117 148 14 318 9 113 157 104 112 116 115 153 147 192 16 159 128 117 141 156 130 318 307 319 113 120 0 0 0 c 56 26 19 7 4 73 2 68 68 55 59 80 8 3 58 48 50 94 113 6 67 6 16 5 59 63 0 0 0 g 69 69 282 8 4 67 63 62 50 55 59 5 9 6 157 76 2 5 73 69 5 7 11 8 59 62 0 0 0 t 101 100 28 10 326 90 121 109 113 117 110 105 179 142 112 60 163 127 16 112 141 12 9 11 112 98 0 0 0
dyads_test_vs_ctrl_m3_shift0 (dyads_test_vs_ctrl_m3)	0.837	0.777	4.096	0.742	0.964	1.737	0.967	7	4	4	5	2	5	3	4.286	3	; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m3; m=1/2; ncol2=28; w=26; offset=0; strand=D; shift=0; score= 4.2857; wwGATawwawwwTAGrwwmwwwwAAAww- ; cor=0.837; Ncor=0.777; logoDP=4.096; NIcor=0.742; NsEucl=0.964; SSD=1.737; NSW=0.967; rcor=7; rNcor=4; rlogoDP=4; rNIcor=5; rNsEucl=2; rSSD=5; rNSW=3; rank_mean=4.286; match_rank=3 a 49 73 12 131 5 69 66 51 52 65 52 63 12 121 14 74 57 52 63 69 52 93 83 129 117 113 66 49 0 c 19 16 7 3 4 20 0 31 33 22 31 28 7 4 4 3 22 26 46 0 21 1 2 8 12 13 14 33 0 g 34 16 115 4 3 23 33 28 27 22 27 4 10 8 119 44 2 1 36 22 35 2 6 4 5 5 25 24 0 t 47 44 15 11 137 37 50 39 37 40 39 54 120 16 12 28 68 70 4 58 41 53 58 8 15 18 44 43 0
dyads_test_vs_ctrl_m5_shift0 (dyads_test_vs_ctrl_m5)	0.810	0.726	3.714	0.685	0.962	1.978	0.962	10	6	9	6	3	11	4	7.000	6	; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m5; m=2/2; ncol2=29; w=26; offset=0; strand=D; shift=0; score= 7; awGATaawwwamTAGrwwmwwwwwAAAww ; cor=0.810; Ncor=0.726; logoDP=3.714; NIcor=0.685; NsEucl=0.962; SSD=1.978; NSW=0.962; rcor=10; rNcor=6; rlogoDP=9; rNIcor=6; rNsEucl=3; rSSD=11; rNSW=4; rank_mean=7.000; match_rank=6 a 58 70 12 130 4 60 71 58 45 65 54 90 21 118 19 69 50 45 56 65 53 90 96 73 118 115 133 47 55 c 21 11 5 2 5 18 20 23 29 17 27 37 8 1 2 5 20 30 48 1 21 1 2 26 10 11 2 24 29 g 33 17 114 6 2 34 20 26 29 20 29 8 9 11 106 44 1 3 33 29 33 3 1 4 2 7 3 23 18 t 32 46 13 6 133 32 33 37 41 42 34 9 106 14 17 26 73 66 7 49 37 50 45 41 14 11 6 50 42

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_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
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=0; ncol=25; watAgAGATAAAaAttaaaawhww- ; Alignment reference a 58 80 42 181 36 194 26 197 12 184 187 162 138 151 50 43 140 134 139 139 53 64 80 73 0 c 43 40 32 1 13 3 6 6 6 6 7 18 19 11 11 26 16 18 21 17 18 55 40 42 0 g 40 43 32 14 144 4 167 5 6 10 8 9 21 24 16 19 23 20 18 24 22 38 28 35 0 t 71 49 106 16 19 11 13 4 188 12 10 23 34 26 135 124 33 40 34 32 119 55 64 62 0

oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5) 0.835 0.768 4.827 0.760 0.955 2.151 0.953 8 5 1 4 6 12 9 6.429 5
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=1/2; ncol2=24; w=23; offset=1; strand=D; shift=1; score= 6.4286; -wwcAAGATAAAaattaaaATcTww ; cor=0.835; Ncor=0.768; logoDP=4.827; NIcor=0.760; NsEucl=0.955; SSD=2.151; NSW=0.953; rcor=8; rNcor=5; rlogoDP=1; rNIcor=4; rNsEucl=6; rSSD=12; rNSW=9; rank_mean=6.429; match_rank=5 a 0 58 55 30 138 138 17 136 7 131 136 118 97 98 25 37 94 101 91 109 20 35 33 44 67 c 0 26 28 78 5 4 9 4 7 4 2 10 13 15 13 16 10 15 14 11 12 75 8 26 25 g 0 28 22 18 2 1 110 6 5 7 4 8 12 16 11 14 19 10 14 10 11 18 6 29 18 t 0 38 45 24 5 7 14 4 131 8 8 14 28 21 101 83 27 24 31 20 107 22 103 51 40

oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc) 0.904 0.565 0.770 -0.123 0.954 0.971 0.968 2 10 16 16 7 2 2 7.857 8
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=2/2; ncol2=15; w=15; offset=0; strand=R; shift=0; score= 7.8571; wwTAGAGATAAAgww---------- ; cor=0.904; Ncor=0.565; logoDP=0.770; NIcor=-0.123; NsEucl=0.954; SSD=0.971; NSW=0.968; rcor=2; rNcor=10; rlogoDP=16; rNIcor=16; rNsEucl=7; rSSD=2; rNSW=2; rank_mean=7.857; match_rank=8 a 180 197 52 525 68 557 48 562 25 524 495 525 97 232 206 0 0 0 0 0 0 0 0 0 0 c 119 101 39 15 45 7 25 8 16 18 39 14 54 80 128 0 0 0 0 0 0 0 0 0 0 g 118 118 36 36 451 16 495 25 21 33 37 26 378 122 89 0 0 0 0 0 0 0 0 0 0 t 196 197 486 37 49 33 45 18 551 38 42 48 84 179 190 0 0 0 0 0 0 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
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)																	; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=0; ncol=25; watAgAGATAAAaAttaaaawhww- ; Alignment reference a 58 80 42 181 36 194 26 197 12 184 187 162 138 151 50 43 140 134 139 139 53 64 80 73 0 c 43 40 32 1 13 3 6 6 6 6 7 18 19 11 11 26 16 18 21 17 18 55 40 42 0 g 40 43 32 14 144 4 167 5 6 10 8 9 21 24 16 19 23 20 18 24 22 38 28 35 0 t 71 49 106 16 19 11 13 4 188 12 10 23 34 26 135 124 33 40 34 32 119 55 64 62 0
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5)	0.835	0.768	4.827	0.760	0.955	2.151	0.953	8	5	1	4	6	12	9	6.429	5	; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=1/2; ncol2=24; w=23; offset=1; strand=D; shift=1; score= 6.4286; -wwcAAGATAAAaattaaaATcTww ; cor=0.835; Ncor=0.768; logoDP=4.827; NIcor=0.760; NsEucl=0.955; SSD=2.151; NSW=0.953; rcor=8; rNcor=5; rlogoDP=1; rNIcor=4; rNsEucl=6; rSSD=12; rNSW=9; rank_mean=6.429; match_rank=5 a 0 58 55 30 138 138 17 136 7 131 136 118 97 98 25 37 94 101 91 109 20 35 33 44 67 c 0 26 28 78 5 4 9 4 7 4 2 10 13 15 13 16 10 15 14 11 12 75 8 26 25 g 0 28 22 18 2 1 110 6 5 7 4 8 12 16 11 14 19 10 14 10 11 18 6 29 18 t 0 38 45 24 5 7 14 4 131 8 8 14 28 21 101 83 27 24 31 20 107 22 103 51 40
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc)	0.904	0.565	0.770	-0.123	0.954	0.971	0.968	2	10	16	16	7	2	2	7.857	8	; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=2/2; ncol2=15; w=15; offset=0; strand=R; shift=0; score= 7.8571; wwTAGAGATAAAgww---------- ; cor=0.904; Ncor=0.565; logoDP=0.770; NIcor=-0.123; NsEucl=0.954; SSD=0.971; NSW=0.968; rcor=2; rNcor=10; rlogoDP=16; rNIcor=16; rNsEucl=7; rSSD=2; rNSW=2; rank_mean=7.857; match_rank=8 a 180 197 52 525 68 557 48 562 25 524 495 525 97 232 206 0 0 0 0 0 0 0 0 0 0 c 119 101 39 15 45 7 25 8 16 18 39 14 54 80 128 0 0 0 0 0 0 0 0 0 0 g 118 118 36 36 451 16 495 25 21 33 37 26 378 122 89 0 0 0 0 0 0 0 0 0 0 t 196 197 486 37 49 33 45 18 551 38 42 48 84 179 190 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift4 ; 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
oligos_6nt_test_vs_ctrl_m3_shift4 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=24; shift=4; ncol=28; ----wwaaTtTTTATCAGATAAAwAwww ; Alignment reference a 0 0 0 0 43 51 73 75 17 31 18 9 17 104 6 14 114 13 107 6 113 101 91 73 88 33 48 42 c 0 0 0 0 20 21 17 12 13 10 8 5 6 5 12 87 2 7 9 6 4 6 12 14 8 10 21 20 g 0 0 0 0 18 18 16 20 5 13 10 12 8 7 11 5 2 98 4 4 3 6 8 8 13 7 20 24 t 0 0 0 0 47 38 22 21 93 74 92 102 97 12 99 22 10 10 8 112 8 15 17 33 19 78 39 42

oligos_7nt_test_vs_ctrl_m1_rc_shift10 (oligos_7nt_test_vs_ctrl_m1_rc) 0.889 0.592 2.493 0.168 0.951 1.243 0.961 4 9 12 12 9 4 5 7.857 9
; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1_rc; m=1/2; ncol2=16; w=16; offset=6; strand=R; shift=10; score= 7.8571; ----------wwTATCAGATAAAgww-- ; cor=0.889; Ncor=0.592; logoDP=2.493; NIcor=0.168; NsEucl=0.951; SSD=1.243; NSW=0.961; rcor=4; rNcor=9; rlogoDP=12; rNIcor=12; rNsEucl=9; rSSD=4; rNSW=5; rank_mean=7.857; match_rank=9 a 0 0 0 0 0 0 0 0 0 0 123 158 51 392 26 37 407 34 407 15 394 353 351 76 153 161 0 0 c 0 0 0 0 0 0 0 0 0 0 78 69 35 18 16 357 2 19 16 18 14 29 31 44 72 89 0 0 g 0 0 0 0 0 0 0 0 0 0 105 75 40 16 29 25 6 379 15 14 16 29 28 230 94 69 0 0 t 0 0 0 0 0 0 0 0 0 0 146 150 326 26 381 33 37 20 14 405 28 41 42 102 133 133 0 0

oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc) 0.772 0.551 1.794 0.125 0.941 2.800 0.930 14 11 13 14 13 15 13 13.286 14
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4_rc; m=2/2; ncol2=24; w=20; offset=-4; strand=R; shift=0; score=13.2857; wwttTTaattTTTATCATCTAAww---- ; cor=0.772; Ncor=0.551; logoDP=1.794; NIcor=0.125; NsEucl=0.941; SSD=2.800; NSW=0.930; rcor=14; rNcor=11; rlogoDP=13; rNIcor=14; rNsEucl=13; rSSD=15; rNSW=13; rank_mean=13.286; match_rank=14 a 50 48 22 24 22 25 78 94 27 24 15 15 12 121 16 12 119 6 19 13 105 104 60 57 0 0 0 0 c 31 31 9 16 8 10 25 8 17 17 8 3 7 7 7 110 8 7 104 7 17 15 26 26 0 0 0 0 g 25 18 20 11 9 9 15 17 11 9 7 8 1 11 8 5 5 8 7 3 13 10 24 23 0 0 0 0 t 45 54 100 100 112 107 33 32 96 101 121 125 131 12 120 24 19 130 21 128 16 22 41 45 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
oligos_6nt_test_vs_ctrl_m3_shift4 (oligos_6nt_test_vs_ctrl_m3)																	; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=24; shift=4; ncol=28; ----wwaaTtTTTATCAGATAAAwAwww ; Alignment reference a 0 0 0 0 43 51 73 75 17 31 18 9 17 104 6 14 114 13 107 6 113 101 91 73 88 33 48 42 c 0 0 0 0 20 21 17 12 13 10 8 5 6 5 12 87 2 7 9 6 4 6 12 14 8 10 21 20 g 0 0 0 0 18 18 16 20 5 13 10 12 8 7 11 5 2 98 4 4 3 6 8 8 13 7 20 24 t 0 0 0 0 47 38 22 21 93 74 92 102 97 12 99 22 10 10 8 112 8 15 17 33 19 78 39 42
oligos_7nt_test_vs_ctrl_m1_rc_shift10 (oligos_7nt_test_vs_ctrl_m1_rc)	0.889	0.592	2.493	0.168	0.951	1.243	0.961	4	9	12	12	9	4	5	7.857	9	; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1_rc; m=1/2; ncol2=16; w=16; offset=6; strand=R; shift=10; score= 7.8571; ----------wwTATCAGATAAAgww-- ; cor=0.889; Ncor=0.592; logoDP=2.493; NIcor=0.168; NsEucl=0.951; SSD=1.243; NSW=0.961; rcor=4; rNcor=9; rlogoDP=12; rNIcor=12; rNsEucl=9; rSSD=4; rNSW=5; rank_mean=7.857; match_rank=9 a 0 0 0 0 0 0 0 0 0 0 123 158 51 392 26 37 407 34 407 15 394 353 351 76 153 161 0 0 c 0 0 0 0 0 0 0 0 0 0 78 69 35 18 16 357 2 19 16 18 14 29 31 44 72 89 0 0 g 0 0 0 0 0 0 0 0 0 0 105 75 40 16 29 25 6 379 15 14 16 29 28 230 94 69 0 0 t 0 0 0 0 0 0 0 0 0 0 146 150 326 26 381 33 37 20 14 405 28 41 42 102 133 133 0 0
oligos_6nt_test_vs_ctrl_m4_rc_shift0 (oligos_6nt_test_vs_ctrl_m4_rc)	0.772	0.551	1.794	0.125	0.941	2.800	0.930	14	11	13	14	13	15	13	13.286	14	; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m4_rc; m=2/2; ncol2=24; w=20; offset=-4; strand=R; shift=0; score=13.2857; wwttTTaattTTTATCATCTAAww---- ; cor=0.772; Ncor=0.551; logoDP=1.794; NIcor=0.125; NsEucl=0.941; SSD=2.800; NSW=0.930; rcor=14; rNcor=11; rlogoDP=13; rNIcor=14; rNsEucl=13; rSSD=15; rNSW=13; rank_mean=13.286; match_rank=14 a 50 48 22 24 22 25 78 94 27 24 15 15 12 121 16 12 119 6 19 13 105 104 60 57 0 0 0 0 c 31 31 9 16 8 10 25 8 17 17 8 3 7 7 7 110 8 7 104 7 17 15 26 26 0 0 0 0 g 25 18 20 11 9 9 15 17 11 9 7 8 1 11 8 5 5 8 7 3 13 10 24 23 0 0 0 0 t 45 54 100 100 112 107 33 32 96 101 121 125 131 12 120 24 19 130 21 128 16 22 41 45 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift0 ; 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_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=0; ncol=27; wwTTAGATGATAAAaattAAaaww--- ; Alignment reference a 45 41 22 16 128 21 130 19 24 120 12 131 125 121 101 96 32 33 107 112 100 100 54 45 0 0 0 c 23 24 10 13 3 7 8 5 5 8 11 1 8 7 9 11 17 15 9 9 11 20 18 25 0 0 0 g 26 26 15 17 7 104 7 8 110 7 7 7 3 8 17 17 8 25 10 8 16 9 31 31 0 0 0 t 57 60 104 105 13 19 6 119 12 16 121 12 15 15 24 27 94 78 25 22 24 22 48 50 0 0 0

oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2) 0.890 0.445 3.895 0.427 0.941 0.986 0.959 3 13 8 9 12 3 7 7.857 7
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=1/3; ncol2=12; w=12; offset=1; strand=D; shift=1; score= 7.8571; -wwTAGATGATaw-------------- ; cor=0.890; Ncor=0.445; logoDP=3.895; NIcor=0.427; NsEucl=0.941; SSD=0.986; NSW=0.959; rcor=3; rNcor=13; rlogoDP=8; rNIcor=9; rNsEucl=12; rSSD=3; rNSW=7; rank_mean=7.857; match_rank=7 a 0 141 192 34 458 21 451 16 59 432 7 231 160 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 74 55 15 6 6 6 4 16 7 12 52 85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 109 103 28 1 402 10 8 345 12 6 80 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 150 124 397 9 45 7 446 54 23 449 111 172 0 0 0 0 0 0 0 0 0 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m5_shift3 (oligos_6nt_test_vs_ctrl_m5) 0.777 0.604 3.915 0.590 0.943 2.817 0.933 13 7 7 7 10 16 12 10.286 11
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=2/3; ncol2=24; w=21; offset=3; strand=D; shift=3; score=10.2857; ---wwcAAGATAAAaattaaaATcTww ; cor=0.777; Ncor=0.604; logoDP=3.915; NIcor=0.590; NsEucl=0.943; SSD=2.817; NSW=0.933; rcor=13; rNcor=7; rlogoDP=7; rNIcor=7; rNsEucl=10; rSSD=16; rNSW=12; rank_mean=10.286; match_rank=11 a 0 0 0 58 55 30 138 138 17 136 7 131 136 118 97 98 25 37 94 101 91 109 20 35 33 44 67 c 0 0 0 26 28 78 5 4 9 4 7 4 2 10 13 15 13 16 10 15 14 11 12 75 8 26 25 g 0 0 0 28 22 18 2 1 110 6 5 7 4 8 12 16 11 14 19 10 14 10 11 18 6 29 18 t 0 0 0 38 45 24 5 7 14 4 131 8 8 14 28 21 101 83 27 24 31 20 107 22 103 51 40

oligos_7nt_test_vs_ctrl_m5_shift2 (oligos_7nt_test_vs_ctrl_m5) 0.763 0.477 4.051 0.466 0.927 2.421 0.919 16 12 5 8 14 14 15 12.000 13
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5; m=3/3; ncol2=15; w=15; offset=2; strand=D; shift=2; score= 12; --wwtaATGATAAAgww---------- ; cor=0.763; Ncor=0.477; logoDP=4.051; NIcor=0.466; NsEucl=0.927; SSD=2.421; NSW=0.919; rcor=16; rNcor=12; rlogoDP=5; rNIcor=8; rNsEucl=14; rSSD=14; rNSW=15; rank_mean=12.000; match_rank=13 a 0 0 168 208 113 323 506 48 47 509 9 514 507 439 95 229 166 0 0 0 0 0 0 0 0 0 0 c 0 0 100 99 61 57 17 14 18 12 12 8 14 29 43 81 122 0 0 0 0 0 0 0 0 0 0 g 0 0 128 105 69 83 17 9 460 15 13 14 14 23 356 82 77 0 0 0 0 0 0 0 0 0 0 t 0 0 163 147 316 96 19 488 34 23 525 23 24 68 65 167 194 0 0 0 0 0 0 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
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)																	; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=0; ncol=27; wwTTAGATGATAAAaattAAaaww--- ; Alignment reference a 45 41 22 16 128 21 130 19 24 120 12 131 125 121 101 96 32 33 107 112 100 100 54 45 0 0 0 c 23 24 10 13 3 7 8 5 5 8 11 1 8 7 9 11 17 15 9 9 11 20 18 25 0 0 0 g 26 26 15 17 7 104 7 8 110 7 7 7 3 8 17 17 8 25 10 8 16 9 31 31 0 0 0 t 57 60 104 105 13 19 6 119 12 16 121 12 15 15 24 27 94 78 25 22 24 22 48 50 0 0 0
oligos_7nt_test_vs_ctrl_m2_shift1 (oligos_7nt_test_vs_ctrl_m2)	0.890	0.445	3.895	0.427	0.941	0.986	0.959	3	13	8	9	12	3	7	7.857	7	; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m2; m=1/3; ncol2=12; w=12; offset=1; strand=D; shift=1; score= 7.8571; -wwTAGATGATaw-------------- ; cor=0.890; Ncor=0.445; logoDP=3.895; NIcor=0.427; NsEucl=0.941; SSD=0.986; NSW=0.959; rcor=3; rNcor=13; rlogoDP=8; rNIcor=9; rNsEucl=12; rSSD=3; rNSW=7; rank_mean=7.857; match_rank=7 a 0 141 192 34 458 21 451 16 59 432 7 231 160 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 74 55 15 6 6 6 4 16 7 12 52 85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 109 103 28 1 402 10 8 345 12 6 80 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 150 124 397 9 45 7 446 54 23 449 111 172 0 0 0 0 0 0 0 0 0 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m5_shift3 (oligos_6nt_test_vs_ctrl_m5)	0.777	0.604	3.915	0.590	0.943	2.817	0.933	13	7	7	7	10	16	12	10.286	11	; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=2/3; ncol2=24; w=21; offset=3; strand=D; shift=3; score=10.2857; ---wwcAAGATAAAaattaaaATcTww ; cor=0.777; Ncor=0.604; logoDP=3.915; NIcor=0.590; NsEucl=0.943; SSD=2.817; NSW=0.933; rcor=13; rNcor=7; rlogoDP=7; rNIcor=7; rNsEucl=10; rSSD=16; rNSW=12; rank_mean=10.286; match_rank=11 a 0 0 0 58 55 30 138 138 17 136 7 131 136 118 97 98 25 37 94 101 91 109 20 35 33 44 67 c 0 0 0 26 28 78 5 4 9 4 7 4 2 10 13 15 13 16 10 15 14 11 12 75 8 26 25 g 0 0 0 28 22 18 2 1 110 6 5 7 4 8 12 16 11 14 19 10 14 10 11 18 6 29 18 t 0 0 0 38 45 24 5 7 14 4 131 8 8 14 28 21 101 83 27 24 31 20 107 22 103 51 40
oligos_7nt_test_vs_ctrl_m5_shift2 (oligos_7nt_test_vs_ctrl_m5)	0.763	0.477	4.051	0.466	0.927	2.421	0.919	16	12	5	8	14	14	15	12.000	13	; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m5; m=3/3; ncol2=15; w=15; offset=2; strand=D; shift=2; score= 12; --wwtaATGATAAAgww---------- ; cor=0.763; Ncor=0.477; logoDP=4.051; NIcor=0.466; NsEucl=0.927; SSD=2.421; NSW=0.919; rcor=16; rNcor=12; rlogoDP=5; rNIcor=8; rNsEucl=14; rSSD=14; rNSW=15; rank_mean=12.000; match_rank=13 a 0 0 168 208 113 323 506 48 47 509 9 514 507 439 95 229 166 0 0 0 0 0 0 0 0 0 0 c 0 0 100 99 61 57 17 14 18 12 12 8 14 29 43 81 122 0 0 0 0 0 0 0 0 0 0 g 0 0 128 105 69 83 17 9 460 15 13 14 14 23 356 82 77 0 0 0 0 0 0 0 0 0 0 t 0 0 163 147 316 96 19 488 34 23 525 23 24 68 65 167 194 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift6 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
dyads_test_vs_ctrl_m1_shift6 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=20; shift=6; ncol=26; ------wwTATCwwwwhwdwyATCww ; Alignment reference a 0 0 0 0 0 0 109 113 28 401 11 28 158 107 124 110 137 135 158 138 16 395 10 15 116 114 c 0 0 0 0 0 0 76 75 30 7 6 369 2 66 97 78 108 80 12 80 172 4 6 373 50 98 g 0 0 0 0 0 0 87 73 15 4 3 11 50 103 58 100 61 47 108 8 73 5 5 16 38 74 t 0 0 0 0 0 0 145 156 344 5 397 9 207 141 138 129 111 155 139 191 156 13 396 13 213 131

dyads_test_vs_ctrl_m2_rc_shift0 (dyads_test_vs_ctrl_m2_rc) 0.778 0.599 1.410 0.137 0.951 1.919 0.952 12 8 14 13 8 9 10 10.571 12
; dyads_test_vs_ctrl_m1 versus dyads_test_vs_ctrl_m2_rc; m=1/2; ncol2=26; w=20; offset=-6; strand=R; shift=0; score=10.5714; wwTTTwwkdwtmwwwwwwwwwATCww ; cor=0.778; Ncor=0.599; logoDP=1.410; NIcor=0.137; NsEucl=0.951; SSD=1.919; NSW=0.952; rcor=12; rNcor=8; rlogoDP=14; rNIcor=13; rNsEucl=8; rSSD=9; rNSW=10; rank_mean=10.571; match_rank=12 a 98 112 11 9 12 141 112 16 127 163 60 112 142 179 105 110 117 113 109 121 90 326 10 28 100 101 c 62 59 8 11 7 5 69 73 5 2 76 157 6 9 5 59 55 50 62 63 67 4 8 282 69 69 g 63 59 5 16 6 67 6 113 94 50 48 58 3 8 80 59 55 68 68 2 73 4 7 19 26 56 t 120 113 319 307 318 130 156 141 117 128 159 16 192 147 153 115 116 112 104 157 113 9 318 14 148 117

oligos_7nt_test_vs_ctrl_m5_rc_shift3 (oligos_7nt_test_vs_ctrl_m5_rc) 0.788 0.411 0.859 0.013 0.922 1.759 0.927 11 16 15 15 16 7 14 13.429 15
; dyads_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5_rc; m=2/2; ncol2=15; w=12; offset=-3; strand=R; shift=3; score=13.4286; ---wwcTTTATCATtaww-------- ; cor=0.788; Ncor=0.411; logoDP=0.859; NIcor=0.013; NsEucl=0.922; SSD=1.759; NSW=0.927; rcor=11; rNcor=16; rlogoDP=15; rNIcor=15; rNsEucl=16; rSSD=7; rNSW=14; rank_mean=13.429; match_rank=15 a 0 0 0 194 167 65 68 24 23 525 23 34 488 19 96 316 147 163 0 0 0 0 0 0 0 0 c 0 0 0 77 82 356 23 14 14 13 15 460 9 17 83 69 105 128 0 0 0 0 0 0 0 0 g 0 0 0 122 81 43 29 14 8 12 12 18 14 17 57 61 99 100 0 0 0 0 0 0 0 0 t 0 0 0 166 229 95 439 507 514 9 509 47 48 506 323 113 208 168 0 0 0 0 0 0 0 0