One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 8 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=13; shift=0; ncol=16; ssCcCCGCCCCss--- ; Alignment reference a 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 c 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 g 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 t 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0

MA0079.3_shift1 (SP1) 0.901 0.763 4.496 0.760 0.939 0.899 0.959 1 1 7 1 3 3 3 2.714 1
; oligos_7nt_test_vs_ctrl_m3 versus MA0079.3 (SP1); m=1/7; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 2.7143; -gCCCCkCCCCy---- ; cor=0.901; Ncor=0.763; logoDP=4.496; NIcor=0.760; NsEucl=0.939; SSD=0.899; NSW=0.959; rcor=1; rNcor=1; rlogoDP=7; rNIcor=1; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.714; match_rank=1 a 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0

MA0516.1_shift1 (SP2) 0.886 0.665 4.462 0.671 0.940 1.034 0.957 5 7 8 5 2 7 4 5.429 3
; oligos_7nt_test_vs_ctrl_m3 versus MA0516.1 (SP2); m=2/7; ncol2=15; w=12; offset=1; strand=D; shift=1; score= 5.4286; -gyCCCGCCyCyyccs ; cor=0.886; Ncor=0.665; logoDP=4.462; NIcor=0.671; NsEucl=0.940; SSD=1.034; NSW=0.957; rcor=5; rNcor=7; rlogoDP=8; rNIcor=5; rNsEucl=2; rSSD=7; rNSW=4; rank_mean=5.429; match_rank=3 a 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316

MA0079.2_shift2 (SP1) 0.870 0.670 3.144 0.647 0.928 1.034 0.948 9 6 18 8 17 8 8 10.571 8
; oligos_7nt_test_vs_ctrl_m3 versus MA0079.2 (SP1); m=3/7; ncol2=10; w=10; offset=2; strand=D; shift=2; score=10.5714; --CCCCkCCCCC---- ; cor=0.870; Ncor=0.670; logoDP=3.144; NIcor=0.647; NsEucl=0.928; SSD=1.034; NSW=0.948; rcor=9; rNcor=6; rlogoDP=18; rNIcor=8; rNsEucl=17; rSSD=8; rNSW=8; rank_mean=10.571; match_rank=8 a 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0

MA0162.2_shift1 (EGR1) 0.848 0.678 3.726 0.664 0.932 1.320 0.945 15 5 14 6 11 16 10 11.000 9
; oligos_7nt_test_vs_ctrl_m3 versus MA0162.2 (EGR1); m=4/7; ncol2=14; w=12; offset=1; strand=D; shift=1; score= 11; -sccCCgCCCMCkCc- ; cor=0.848; Ncor=0.678; logoDP=3.726; NIcor=0.664; NsEucl=0.932; SSD=1.320; NSW=0.945; rcor=15; rNcor=5; rlogoDP=14; rNIcor=6; rNsEucl=11; rSSD=16; rNSW=10; rank_mean=11.000; match_rank=9 a 0 1098 1506 1160 1335 233 2911 0 0 0 3652 0 2368 0 3026 0 c 0 5728 6847 6049 10431 11574 0 12256 11852 10154 8361 11952 0 9849 5595 0 g 0 3083 1359 2250 0 0 6840 0 0 611 0 0 6599 1420 1913 0 t 0 2347 2544 2797 490 449 2505 0 404 1491 243 304 3289 987 1722 0

MA0599.1_shift1 (KLF5) 0.852 0.655 4.321 0.636 0.920 1.279 0.936 13 8 9 9 21 13 18 13.000 11
; oligos_7nt_test_vs_ctrl_m3 versus MA0599.1 (KLF5); m=5/7; ncol2=10; w=10; offset=1; strand=D; shift=1; score= 13; -gCCMCrCCCh----- ; cor=0.852; Ncor=0.655; logoDP=4.321; NIcor=0.636; NsEucl=0.920; SSD=1.279; NSW=0.936; rcor=13; rNcor=8; rlogoDP=9; rNIcor=9; rNsEucl=21; rSSD=13; rNSW=18; rank_mean=13.000; match_rank=11 a 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0

MA0079.1_rc_shift1 (SP1_rc) 0.770 0.592 0.961 -0.075 0.910 1.628 0.919 32 13 32 33 29 23 29 27.286 30
; oligos_7nt_test_vs_ctrl_m3 versus MA0079.1_rc (SP1_rc); m=6/7; ncol2=10; w=10; offset=1; strand=R; shift=1; score=27.2857; -WCMmhsCCym----- ; cor=0.770; Ncor=0.592; logoDP=0.961; NIcor=-0.075; NsEucl=0.910; SSD=1.628; NSW=0.919; rcor=32; rNcor=13; rlogoDP=32; rNIcor=33; rNsEucl=29; rSSD=23; rNSW=29; rank_mean=27.286; match_rank=30 a 0 6 0 2 2 2 1 0 0 1 2 0 0 0 0 0 c 0 0 6 6 5 4 2 8 8 4 4 0 0 0 0 0 g 0 0 1 0 1 0 5 0 0 1 1 0 0 0 0 0 t 0 2 1 0 0 2 0 0 0 2 1 0 0 0 0 0

MA0039.2_rc_shift1 (Klf4_rc) 0.791 0.608 2.178 0.045 0.905 1.805 0.910 29 11 28 27 34 30 32 27.286 31
; oligos_7nt_test_vs_ctrl_m3 versus MA0039.2_rc (Klf4_rc); m=7/7; ncol2=10; w=10; offset=1; strand=R; shift=1; score=27.2857; -gCCmCrCCCw----- ; cor=0.791; Ncor=0.608; logoDP=2.178; NIcor=0.045; NsEucl=0.905; SSD=1.805; NSW=0.910; rcor=29; rNcor=11; rlogoDP=28; rNIcor=27; rNsEucl=34; rSSD=30; rNSW=32; rank_mean=27.286; match_rank=31 a 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 254 123 264 42 22 277 14 14 88 1468 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_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)																	; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=13; shift=0; ncol=16; ssCcCCGCCCCss--- ; Alignment reference a 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 c 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 g 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 t 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0
MA0079.3_shift1 (SP1)	0.901	0.763	4.496	0.760	0.939	0.899	0.959	1	1	7	1	3	3	3	2.714	1	; oligos_7nt_test_vs_ctrl_m3 versus MA0079.3 (SP1); m=1/7; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 2.7143; -gCCCCkCCCCy---- ; cor=0.901; Ncor=0.763; logoDP=4.496; NIcor=0.760; NsEucl=0.939; SSD=0.899; NSW=0.959; rcor=1; rNcor=1; rlogoDP=7; rNIcor=1; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.714; match_rank=1 a 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0
MA0516.1_shift1 (SP2)	0.886	0.665	4.462	0.671	0.940	1.034	0.957	5	7	8	5	2	7	4	5.429	3	; oligos_7nt_test_vs_ctrl_m3 versus MA0516.1 (SP2); m=2/7; ncol2=15; w=12; offset=1; strand=D; shift=1; score= 5.4286; -gyCCCGCCyCyyccs ; cor=0.886; Ncor=0.665; logoDP=4.462; NIcor=0.671; NsEucl=0.940; SSD=1.034; NSW=0.957; rcor=5; rNcor=7; rlogoDP=8; rNIcor=5; rNsEucl=2; rSSD=7; rNSW=4; rank_mean=5.429; match_rank=3 a 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316
MA0079.2_shift2 (SP1)	0.870	0.670	3.144	0.647	0.928	1.034	0.948	9	6	18	8	17	8	8	10.571	8	; oligos_7nt_test_vs_ctrl_m3 versus MA0079.2 (SP1); m=3/7; ncol2=10; w=10; offset=2; strand=D; shift=2; score=10.5714; --CCCCkCCCCC---- ; cor=0.870; Ncor=0.670; logoDP=3.144; NIcor=0.647; NsEucl=0.928; SSD=1.034; NSW=0.948; rcor=9; rNcor=6; rlogoDP=18; rNIcor=8; rNsEucl=17; rSSD=8; rNSW=8; rank_mean=10.571; match_rank=8 a 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0
MA0162.2_shift1 (EGR1)	0.848	0.678	3.726	0.664	0.932	1.320	0.945	15	5	14	6	11	16	10	11.000	9	; oligos_7nt_test_vs_ctrl_m3 versus MA0162.2 (EGR1); m=4/7; ncol2=14; w=12; offset=1; strand=D; shift=1; score= 11; -sccCCgCCCMCkCc- ; cor=0.848; Ncor=0.678; logoDP=3.726; NIcor=0.664; NsEucl=0.932; SSD=1.320; NSW=0.945; rcor=15; rNcor=5; rlogoDP=14; rNIcor=6; rNsEucl=11; rSSD=16; rNSW=10; rank_mean=11.000; match_rank=9 a 0 1098 1506 1160 1335 233 2911 0 0 0 3652 0 2368 0 3026 0 c 0 5728 6847 6049 10431 11574 0 12256 11852 10154 8361 11952 0 9849 5595 0 g 0 3083 1359 2250 0 0 6840 0 0 611 0 0 6599 1420 1913 0 t 0 2347 2544 2797 490 449 2505 0 404 1491 243 304 3289 987 1722 0
MA0599.1_shift1 (KLF5)	0.852	0.655	4.321	0.636	0.920	1.279	0.936	13	8	9	9	21	13	18	13.000	11	; oligos_7nt_test_vs_ctrl_m3 versus MA0599.1 (KLF5); m=5/7; ncol2=10; w=10; offset=1; strand=D; shift=1; score= 13; -gCCMCrCCCh----- ; cor=0.852; Ncor=0.655; logoDP=4.321; NIcor=0.636; NsEucl=0.920; SSD=1.279; NSW=0.936; rcor=13; rNcor=8; rlogoDP=9; rNIcor=9; rNsEucl=21; rSSD=13; rNSW=18; rank_mean=13.000; match_rank=11 a 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0
MA0079.1_rc_shift1 (SP1_rc)	0.770	0.592	0.961	-0.075	0.910	1.628	0.919	32	13	32	33	29	23	29	27.286	30	; oligos_7nt_test_vs_ctrl_m3 versus MA0079.1_rc (SP1_rc); m=6/7; ncol2=10; w=10; offset=1; strand=R; shift=1; score=27.2857; -WCMmhsCCym----- ; cor=0.770; Ncor=0.592; logoDP=0.961; NIcor=-0.075; NsEucl=0.910; SSD=1.628; NSW=0.919; rcor=32; rNcor=13; rlogoDP=32; rNIcor=33; rNsEucl=29; rSSD=23; rNSW=29; rank_mean=27.286; match_rank=30 a 0 6 0 2 2 2 1 0 0 1 2 0 0 0 0 0 c 0 0 6 6 5 4 2 8 8 4 4 0 0 0 0 0 g 0 0 1 0 1 0 5 0 0 1 1 0 0 0 0 0 t 0 2 1 0 0 2 0 0 0 2 1 0 0 0 0 0
MA0039.2_rc_shift1 (Klf4_rc)	0.791	0.608	2.178	0.045	0.905	1.805	0.910	29	11	28	27	34	30	32	27.286	31	; oligos_7nt_test_vs_ctrl_m3 versus MA0039.2_rc (Klf4_rc); m=7/7; ncol2=10; w=10; offset=1; strand=R; shift=1; score=27.2857; -gCCmCrCCCw----- ; cor=0.791; Ncor=0.608; logoDP=2.178; NIcor=0.045; NsEucl=0.905; SSD=1.805; NSW=0.910; rcor=29; rNcor=11; rlogoDP=28; rNIcor=27; rNsEucl=34; rSSD=30; rNSW=32; rank_mean=27.286; match_rank=31 a 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift2 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_test_vs_ctrl_m1_shift2 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=2; ncol=16; --csGCCCCaGGgcss ; Alignment reference a 0 0 195 244 54 37 19 21 11 808 21 17 123 132 281 174 c 0 0 548 431 70 1140 1083 1093 1108 179 89 101 283 849 359 410 g 0 0 314 350 1071 58 138 117 132 248 1147 1134 747 185 425 448 t 0 0 210 242 72 32 27 36 16 32 10 15 114 101 202 235

MA0524.1_shift0 (TFAP2C) 0.883 0.717 5.323 0.719 0.944 1.048 0.960 7 3 5 3 1 9 2 4.286 2
; oligos_7nt_test_vs_ctrl_m1 versus MA0524.1 (TFAP2C); m=1/3; ncol2=15; w=13; offset=-2; strand=D; shift=0; score= 4.2857; hmydsCCyCAGGsca- ; cor=0.883; Ncor=0.717; logoDP=5.323; NIcor=0.719; NsEucl=0.944; SSD=1.048; NSW=0.960; rcor=7; rNcor=3; rlogoDP=5; rNIcor=3; rNsEucl=1; rSSD=9; rNSW=2; rank_mean=4.286; match_rank=2 a 4801 6477 2550 4918 421 0 0 0 1082 16442 191 0 285 4343 8905 0 c 6752 4693 4943 2009 6040 18426 14817 9317 14790 0 0 0 7908 9235 3259 0 g 2123 3347 2643 6098 11033 0 0 1237 1768 1195 18235 18426 10222 1788 2536 0 t 4750 3909 8290 5401 932 0 3609 7872 786 789 0 0 11 3060 3726 0

MA0003.2_shift0 (TFAP2A) 0.841 0.684 5.056 0.681 0.935 1.441 0.945 16 4 6 4 7 20 11 9.714 6
; oligos_7nt_test_vs_ctrl_m1 versus MA0003.2 (TFAP2A); m=2/3; ncol2=15; w=13; offset=-2; strand=D; shift=0; score= 9.7143; maywGCCysAGGsCa- ; cor=0.841; Ncor=0.684; logoDP=5.056; NIcor=0.681; NsEucl=0.935; SSD=1.441; NSW=0.945; rcor=16; rNcor=4; rlogoDP=6; rNIcor=4; rNsEucl=7; rSSD=20; rNSW=11; rank_mean=9.714; match_rank=6 a 1387 2141 727 1517 56 0 0 62 346 3738 460 0 116 451 3146 0 c 1630 1060 1506 519 1199 5098 4762 1736 2729 236 0 0 1443 3672 690 0 g 851 792 884 985 3712 0 0 85 1715 920 4638 5098 3455 465 168 0 t 1230 1105 1981 2077 131 0 336 3215 308 204 0 0 84 510 1094 0

MA0003.1_shift4 (TFAP2A) 0.818 0.526 3.671 0.485 0.909 1.351 0.925 21 19 15 17 31 18 27 21.143 19
; oligos_7nt_test_vs_ctrl_m1 versus MA0003.1 (TFAP2A); m=3/3; ncol2=9; w=9; offset=2; strand=D; shift=4; score=21.1429; ----GCCcbrrGs--- ; cor=0.818; Ncor=0.526; logoDP=3.671; NIcor=0.485; NsEucl=0.909; SSD=1.351; NSW=0.925; rcor=21; rNcor=19; rlogoDP=15; rNIcor=17; rNsEucl=31; rSSD=18; rNSW=27; rank_mean=21.143; match_rank=19 a 0 0 0 0 0 0 0 22 19 55 53 19 9 0 0 0 c 0 0 0 0 0 185 185 71 57 44 30 16 78 0 0 0 g 0 0 0 0 185 0 0 46 61 67 91 137 79 0 0 0 t 0 0 0 0 0 0 0 46 48 19 11 13 19 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_7nt_test_vs_ctrl_m1_shift2 (oligos_7nt_test_vs_ctrl_m1)																	; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=2; ncol=16; --csGCCCCaGGgcss ; Alignment reference a 0 0 195 244 54 37 19 21 11 808 21 17 123 132 281 174 c 0 0 548 431 70 1140 1083 1093 1108 179 89 101 283 849 359 410 g 0 0 314 350 1071 58 138 117 132 248 1147 1134 747 185 425 448 t 0 0 210 242 72 32 27 36 16 32 10 15 114 101 202 235
MA0524.1_shift0 (TFAP2C)	0.883	0.717	5.323	0.719	0.944	1.048	0.960	7	3	5	3	1	9	2	4.286	2	; oligos_7nt_test_vs_ctrl_m1 versus MA0524.1 (TFAP2C); m=1/3; ncol2=15; w=13; offset=-2; strand=D; shift=0; score= 4.2857; hmydsCCyCAGGsca- ; cor=0.883; Ncor=0.717; logoDP=5.323; NIcor=0.719; NsEucl=0.944; SSD=1.048; NSW=0.960; rcor=7; rNcor=3; rlogoDP=5; rNIcor=3; rNsEucl=1; rSSD=9; rNSW=2; rank_mean=4.286; match_rank=2 a 4801 6477 2550 4918 421 0 0 0 1082 16442 191 0 285 4343 8905 0 c 6752 4693 4943 2009 6040 18426 14817 9317 14790 0 0 0 7908 9235 3259 0 g 2123 3347 2643 6098 11033 0 0 1237 1768 1195 18235 18426 10222 1788 2536 0 t 4750 3909 8290 5401 932 0 3609 7872 786 789 0 0 11 3060 3726 0
MA0003.2_shift0 (TFAP2A)	0.841	0.684	5.056	0.681	0.935	1.441	0.945	16	4	6	4	7	20	11	9.714	6	; oligos_7nt_test_vs_ctrl_m1 versus MA0003.2 (TFAP2A); m=2/3; ncol2=15; w=13; offset=-2; strand=D; shift=0; score= 9.7143; maywGCCysAGGsCa- ; cor=0.841; Ncor=0.684; logoDP=5.056; NIcor=0.681; NsEucl=0.935; SSD=1.441; NSW=0.945; rcor=16; rNcor=4; rlogoDP=6; rNIcor=4; rNsEucl=7; rSSD=20; rNSW=11; rank_mean=9.714; match_rank=6 a 1387 2141 727 1517 56 0 0 62 346 3738 460 0 116 451 3146 0 c 1630 1060 1506 519 1199 5098 4762 1736 2729 236 0 0 1443 3672 690 0 g 851 792 884 985 3712 0 0 85 1715 920 4638 5098 3455 465 168 0 t 1230 1105 1981 2077 131 0 336 3215 308 204 0 0 84 510 1094 0
MA0003.1_shift4 (TFAP2A)	0.818	0.526	3.671	0.485	0.909	1.351	0.925	21	19	15	17	31	18	27	21.143	19	; oligos_7nt_test_vs_ctrl_m1 versus MA0003.1 (TFAP2A); m=3/3; ncol2=9; w=9; offset=2; strand=D; shift=4; score=21.1429; ----GCCcbrrGs--- ; cor=0.818; Ncor=0.526; logoDP=3.671; NIcor=0.485; NsEucl=0.909; SSD=1.351; NSW=0.925; rcor=21; rNcor=19; rlogoDP=15; rNIcor=17; rNsEucl=31; rSSD=18; rNSW=27; rank_mean=21.143; match_rank=19 a 0 0 0 0 0 0 0 22 19 55 53 19 9 0 0 0 c 0 0 0 0 0 185 185 71 57 44 30 16 78 0 0 0 g 0 0 0 0 185 0 0 46 61 67 91 137 79 0 0 0 t 0 0 0 0 0 0 0 46 48 19 11 13 19 0 0 0

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=15; shift=0; ncol=15; ssGCCbsvsGCCtss ; Alignment reference a 159 182 24 26 22 9 102 311 14 30 18 36 92 122 179 c 456 389 50 1006 972 486 521 367 395 48 1028 924 202 428 334 g 337 330 1014 67 101 308 384 431 700 1010 56 125 258 392 410 t 166 217 30 19 23 315 111 9 9 30 16 33 566 176 195

MA0003.1_shift2 (TFAP2A) 0.890 0.534 4.042 0.521 0.934 0.705 0.961 3 17 10 13 9 1 1 7.714 4
; dyads_test_vs_ctrl_m3 versus MA0003.1 (TFAP2A); m=1/1; ncol2=9; w=9; offset=2; strand=D; shift=2; score= 7.7143; --GCCcbrrGs---- ; cor=0.890; Ncor=0.534; logoDP=4.042; NIcor=0.521; NsEucl=0.934; SSD=0.705; NSW=0.961; rcor=3; rNcor=17; rlogoDP=10; rNIcor=13; rNsEucl=9; rSSD=1; rNSW=1; rank_mean=7.714; match_rank=4 a 0 0 0 0 0 22 19 55 53 19 9 0 0 0 0 c 0 0 0 185 185 71 57 44 30 16 78 0 0 0 0 g 0 0 185 0 0 46 61 67 91 137 79 0 0 0 0 t 0 0 0 0 0 46 48 19 11 13 19 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m3_shift0 (dyads_test_vs_ctrl_m3)																		; dyads_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; ssGCCbsvsGCCtss ; Alignment reference a 159 182 24 26 22 9 102 311 14 30 18 36 92 122 179 c 456 389 50 1006 972 486 521 367 395 48 1028 924 202 428 334 g 337 330 1014 67 101 308 384 431 700 1010 56 125 258 392 410 t 166 217 30 19 23 315 111 9 9 30 16 33 566 176 195
MA0003.1_shift2 (TFAP2A)		0.890	0.534	4.042	0.521	0.934	0.705	0.961	3	17	10	13	9	1	1	7.714	4	; dyads_test_vs_ctrl_m3 versus MA0003.1 (TFAP2A); m=1/1; ncol2=9; w=9; offset=2; strand=D; shift=2; score= 7.7143; --GCCcbrrGs---- ; cor=0.890; Ncor=0.534; logoDP=4.042; NIcor=0.521; NsEucl=0.934; SSD=0.705; NSW=0.961; rcor=3; rNcor=17; rlogoDP=10; rNIcor=13; rNsEucl=9; rSSD=1; rNSW=1; rank_mean=7.714; match_rank=4 a 0 0 0 0 0 22 19 55 53 19 9 0 0 0 0 c 0 0 0 185 185 71 57 44 30 16 78 0 0 0 0 g 0 0 185 0 0 46 61 67 91 137 79 0 0 0 0 t 0 0 0 0 0 46 48 19 11 13 19 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift3 ; 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_7nt_test_vs_ctrl_m2_shift3 (oligos_7nt_test_vs_ctrl_m2)
; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=11; shift=3; ncol=15; ---skCCTCAGGys- ; Alignment reference a 0 0 0 49 57 0 0 1 0 192 0 0 41 50 0 c 0 0 0 81 38 239 239 1 240 20 7 2 89 71 0 g 0 0 0 77 80 1 2 19 1 29 234 239 45 66 0 t 0 0 0 34 66 1 0 220 0 0 0 0 66 54 0

MA0524.1_shift0 (TFAP2C) 0.866 0.635 7.711 0.649 0.929 1.225 0.944 10 10 1 7 14 10 12 9.143 5
; oligos_7nt_test_vs_ctrl_m2 versus MA0524.1 (TFAP2C); m=1/2; ncol2=15; w=11; offset=-3; strand=D; shift=0; score= 9.1429; hmydsCCyCAGGsca ; cor=0.866; Ncor=0.635; logoDP=7.711; NIcor=0.649; NsEucl=0.929; SSD=1.225; NSW=0.944; rcor=10; rNcor=10; rlogoDP=1; rNIcor=7; rNsEucl=14; rSSD=10; rNSW=12; rank_mean=9.143; match_rank=5 a 4801 6477 2550 4918 421 0 0 0 1082 16442 191 0 285 4343 8905 c 6752 4693 4943 2009 6040 18426 14817 9317 14790 0 0 0 7908 9235 3259 g 2123 3347 2643 6098 11033 0 0 1237 1768 1195 18235 18426 10222 1788 2536 t 4750 3909 8290 5401 932 0 3609 7872 786 789 0 0 11 3060 3726

MA0003.2_shift0 (TFAP2A) 0.829 0.608 7.182 0.609 0.920 1.565 0.929 19 12 2 10 22 22 24 15.857 15
; oligos_7nt_test_vs_ctrl_m2 versus MA0003.2 (TFAP2A); m=2/2; ncol2=15; w=11; offset=-3; strand=D; shift=0; score=15.8571; maywGCCysAGGsCa ; cor=0.829; Ncor=0.608; logoDP=7.182; NIcor=0.609; NsEucl=0.920; SSD=1.565; NSW=0.929; rcor=19; rNcor=12; rlogoDP=2; rNIcor=10; rNsEucl=22; rSSD=22; rNSW=24; rank_mean=15.857; match_rank=15 a 1387 2141 727 1517 56 0 0 62 346 3738 460 0 116 451 3146 c 1630 1060 1506 519 1199 5098 4762 1736 2729 236 0 0 1443 3672 690 g 851 792 884 985 3712 0 0 85 1715 920 4638 5098 3455 465 168 t 1230 1105 1981 2077 131 0 336 3215 308 204 0 0 84 510 1094

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_test_vs_ctrl_m2_shift3 (oligos_7nt_test_vs_ctrl_m2)																	; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=11; shift=3; ncol=15; ---skCCTCAGGys- ; Alignment reference a 0 0 0 49 57 0 0 1 0 192 0 0 41 50 0 c 0 0 0 81 38 239 239 1 240 20 7 2 89 71 0 g 0 0 0 77 80 1 2 19 1 29 234 239 45 66 0 t 0 0 0 34 66 1 0 220 0 0 0 0 66 54 0
MA0524.1_shift0 (TFAP2C)	0.866	0.635	7.711	0.649	0.929	1.225	0.944	10	10	1	7	14	10	12	9.143	5	; oligos_7nt_test_vs_ctrl_m2 versus MA0524.1 (TFAP2C); m=1/2; ncol2=15; w=11; offset=-3; strand=D; shift=0; score= 9.1429; hmydsCCyCAGGsca ; cor=0.866; Ncor=0.635; logoDP=7.711; NIcor=0.649; NsEucl=0.929; SSD=1.225; NSW=0.944; rcor=10; rNcor=10; rlogoDP=1; rNIcor=7; rNsEucl=14; rSSD=10; rNSW=12; rank_mean=9.143; match_rank=5 a 4801 6477 2550 4918 421 0 0 0 1082 16442 191 0 285 4343 8905 c 6752 4693 4943 2009 6040 18426 14817 9317 14790 0 0 0 7908 9235 3259 g 2123 3347 2643 6098 11033 0 0 1237 1768 1195 18235 18426 10222 1788 2536 t 4750 3909 8290 5401 932 0 3609 7872 786 789 0 0 11 3060 3726
MA0003.2_shift0 (TFAP2A)	0.829	0.608	7.182	0.609	0.920	1.565	0.929	19	12	2	10	22	22	24	15.857	15	; oligos_7nt_test_vs_ctrl_m2 versus MA0003.2 (TFAP2A); m=2/2; ncol2=15; w=11; offset=-3; strand=D; shift=0; score=15.8571; maywGCCysAGGsCa ; cor=0.829; Ncor=0.608; logoDP=7.182; NIcor=0.609; NsEucl=0.920; SSD=1.565; NSW=0.929; rcor=19; rNcor=12; rlogoDP=2; rNIcor=10; rNsEucl=22; rSSD=22; rNSW=24; rank_mean=15.857; match_rank=15 a 1387 2141 727 1517 56 0 0 62 346 3738 460 0 116 451 3146 c 1630 1060 1506 519 1199 5098 4762 1736 2729 236 0 0 1443 3672 690 g 851 792 884 985 3712 0 0 85 1715 920 4638 5098 3455 465 168 t 1230 1105 1981 2077 131 0 336 3215 308 204 0 0 84 510 1094

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m2_shift0 ; 7 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=17; shift=0; ncol=17; ssgCCCCGCCCCGCCss ; Alignment reference a 239 229 121 81 76 79 109 103 58 57 71 96 98 88 97 187 179 c 726 623 262 1223 1188 1203 1191 103 1270 1239 1224 1096 221 1129 1129 679 609 g 407 484 1065 188 222 230 180 1258 182 216 218 256 1138 270 245 451 559 t 210 246 134 90 96 70 102 118 72 70 69 134 125 95 111 265 235

MA0599.1_shift2 (KLF5) 0.894 0.526 3.877 0.518 0.932 0.936 0.953 2 20 11 14 12 5 5 9.857 7
; dyads_test_vs_ctrl_m2 versus MA0599.1 (KLF5); m=1/6; ncol2=10; w=10; offset=2; strand=D; shift=2; score= 9.8571; --gCCMCrCCCh----- ; cor=0.894; Ncor=0.526; logoDP=3.877; NIcor=0.518; NsEucl=0.932; SSD=0.936; NSW=0.953; rcor=2; rNcor=20; rlogoDP=11; rNIcor=14; rNsEucl=12; rSSD=5; rNSW=5; rank_mean=9.857; match_rank=7 a 0 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0

MA0516.1_shift2 (SP2) 0.822 0.725 3.755 0.720 0.939 1.699 0.943 20 2 13 2 4 25 13 11.286 10
; dyads_test_vs_ctrl_m2 versus MA0516.1 (SP2); m=2/6; ncol2=15; w=15; offset=2; strand=D; shift=2; score=11.2857; --gyCCCGCCyCyyccs ; cor=0.822; Ncor=0.725; logoDP=3.755; NIcor=0.720; NsEucl=0.939; SSD=1.699; NSW=0.943; rcor=20; rNcor=2; rlogoDP=13; rNIcor=2; rNsEucl=4; rSSD=25; rNSW=13; rank_mean=11.286; match_rank=10 a 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316

MA0079.3_shift2 (SP1) 0.857 0.554 3.841 0.551 0.927 1.277 0.942 11 15 12 11 18 12 15 13.429 12
; dyads_test_vs_ctrl_m2 versus MA0079.3 (SP1); m=3/6; ncol2=11; w=11; offset=2; strand=D; shift=2; score=13.4286; --gCCCCkCCCCy---- ; cor=0.857; Ncor=0.554; logoDP=3.841; NIcor=0.551; NsEucl=0.927; SSD=1.277; NSW=0.942; rcor=11; rNcor=15; rlogoDP=12; rNIcor=11; rNsEucl=18; rSSD=12; rNSW=15; rank_mean=13.429; match_rank=12 a 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0

MA0079.2_shift3 (SP1) 0.835 0.491 2.940 0.484 0.919 1.297 0.935 18 27 21 18 23 14 19 20.000 17
; dyads_test_vs_ctrl_m2 versus MA0079.2 (SP1); m=4/6; ncol2=10; w=10; offset=3; strand=D; shift=3; score= 20; ---CCCCkCCCCC---- ; cor=0.835; Ncor=0.491; logoDP=2.940; NIcor=0.484; NsEucl=0.919; SSD=1.297; NSW=0.935; rcor=18; rNcor=27; rlogoDP=21; rNIcor=18; rNsEucl=23; rSSD=14; rNSW=19; rank_mean=20.000; match_rank=17 a 0 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0

MA0039.2_rc_shift2 (Klf4_rc) 0.848 0.499 1.408 -0.011 0.919 1.320 0.934 14 24 29 31 24 17 20 22.714 23
; dyads_test_vs_ctrl_m2 versus MA0039.2_rc (Klf4_rc); m=5/6; ncol2=10; w=10; offset=2; strand=R; shift=2; score=22.7143; --gCCmCrCCCw----- ; cor=0.848; Ncor=0.499; logoDP=1.408; NIcor=-0.011; NsEucl=0.919; SSD=1.320; NSW=0.934; rcor=14; rNcor=24; rlogoDP=29; rNIcor=31; rNsEucl=24; rSSD=17; rNSW=20; rank_mean=22.714; match_rank=23 a 0 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0 0

MA0079.1_rc_shift2 (SP1_rc) 0.760 0.447 0.760 -0.066 0.910 1.635 0.918 38 33 36 32 30 24 30 31.857 35
; dyads_test_vs_ctrl_m2 versus MA0079.1_rc (SP1_rc); m=6/6; ncol2=10; w=10; offset=2; strand=R; shift=2; score=31.8571; --WCMmhsCCym----- ; cor=0.760; Ncor=0.447; logoDP=0.760; NIcor=-0.066; NsEucl=0.910; SSD=1.635; NSW=0.918; rcor=38; rNcor=33; rlogoDP=36; rNIcor=32; rNsEucl=30; rSSD=24; rNSW=30; rank_mean=31.857; match_rank=35 a 0 0 6 0 2 2 2 1 0 0 1 2 0 0 0 0 0 c 0 0 0 6 6 5 4 2 8 8 4 4 0 0 0 0 0 g 0 0 0 1 0 1 0 5 0 0 1 1 0 0 0 0 0 t 0 0 2 1 0 0 2 0 0 0 2 1 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
dyads_test_vs_ctrl_m2_shift0 (dyads_test_vs_ctrl_m2)																	; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; ssgCCCCGCCCCGCCss ; Alignment reference a 239 229 121 81 76 79 109 103 58 57 71 96 98 88 97 187 179 c 726 623 262 1223 1188 1203 1191 103 1270 1239 1224 1096 221 1129 1129 679 609 g 407 484 1065 188 222 230 180 1258 182 216 218 256 1138 270 245 451 559 t 210 246 134 90 96 70 102 118 72 70 69 134 125 95 111 265 235
MA0599.1_shift2 (KLF5)	0.894	0.526	3.877	0.518	0.932	0.936	0.953	2	20	11	14	12	5	5	9.857	7	; dyads_test_vs_ctrl_m2 versus MA0599.1 (KLF5); m=1/6; ncol2=10; w=10; offset=2; strand=D; shift=2; score= 9.8571; --gCCMCrCCCh----- ; cor=0.894; Ncor=0.526; logoDP=3.877; NIcor=0.518; NsEucl=0.932; SSD=0.936; NSW=0.953; rcor=2; rNcor=20; rlogoDP=11; rNIcor=14; rNsEucl=12; rSSD=5; rNSW=5; rank_mean=9.857; match_rank=7 a 0 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0
MA0516.1_shift2 (SP2)	0.822	0.725	3.755	0.720	0.939	1.699	0.943	20	2	13	2	4	25	13	11.286	10	; dyads_test_vs_ctrl_m2 versus MA0516.1 (SP2); m=2/6; ncol2=15; w=15; offset=2; strand=D; shift=2; score=11.2857; --gyCCCGCCyCyyccs ; cor=0.822; Ncor=0.725; logoDP=3.755; NIcor=0.720; NsEucl=0.939; SSD=1.699; NSW=0.943; rcor=20; rNcor=2; rlogoDP=13; rNIcor=2; rNsEucl=4; rSSD=25; rNSW=13; rank_mean=11.286; match_rank=10 a 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316
MA0079.3_shift2 (SP1)	0.857	0.554	3.841	0.551	0.927	1.277	0.942	11	15	12	11	18	12	15	13.429	12	; dyads_test_vs_ctrl_m2 versus MA0079.3 (SP1); m=3/6; ncol2=11; w=11; offset=2; strand=D; shift=2; score=13.4286; --gCCCCkCCCCy---- ; cor=0.857; Ncor=0.554; logoDP=3.841; NIcor=0.551; NsEucl=0.927; SSD=1.277; NSW=0.942; rcor=11; rNcor=15; rlogoDP=12; rNIcor=11; rNsEucl=18; rSSD=12; rNSW=15; rank_mean=13.429; match_rank=12 a 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0
MA0079.2_shift3 (SP1)	0.835	0.491	2.940	0.484	0.919	1.297	0.935	18	27	21	18	23	14	19	20.000	17	; dyads_test_vs_ctrl_m2 versus MA0079.2 (SP1); m=4/6; ncol2=10; w=10; offset=3; strand=D; shift=3; score= 20; ---CCCCkCCCCC---- ; cor=0.835; Ncor=0.491; logoDP=2.940; NIcor=0.484; NsEucl=0.919; SSD=1.297; NSW=0.935; rcor=18; rNcor=27; rlogoDP=21; rNIcor=18; rNsEucl=23; rSSD=14; rNSW=19; rank_mean=20.000; match_rank=17 a 0 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0
MA0039.2_rc_shift2 (Klf4_rc)	0.848	0.499	1.408	-0.011	0.919	1.320	0.934	14	24	29	31	24	17	20	22.714	23	; dyads_test_vs_ctrl_m2 versus MA0039.2_rc (Klf4_rc); m=5/6; ncol2=10; w=10; offset=2; strand=R; shift=2; score=22.7143; --gCCmCrCCCw----- ; cor=0.848; Ncor=0.499; logoDP=1.408; NIcor=-0.011; NsEucl=0.919; SSD=1.320; NSW=0.934; rcor=14; rNcor=24; rlogoDP=29; rNIcor=31; rNsEucl=24; rSSD=17; rNSW=20; rank_mean=22.714; match_rank=23 a 0 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0 0
MA0079.1_rc_shift2 (SP1_rc)	0.760	0.447	0.760	-0.066	0.910	1.635	0.918	38	33	36	32	30	24	30	31.857	35	; dyads_test_vs_ctrl_m2 versus MA0079.1_rc (SP1_rc); m=6/6; ncol2=10; w=10; offset=2; strand=R; shift=2; score=31.8571; --WCMmhsCCym----- ; cor=0.760; Ncor=0.447; logoDP=0.760; NIcor=-0.066; NsEucl=0.910; SSD=1.635; NSW=0.918; rcor=38; rNcor=33; rlogoDP=36; rNIcor=32; rNsEucl=30; rSSD=24; rNSW=30; rank_mean=31.857; match_rank=35 a 0 0 6 0 2 2 2 1 0 0 1 2 0 0 0 0 0 c 0 0 0 6 6 5 4 2 8 8 4 4 0 0 0 0 0 g 0 0 0 1 0 1 0 5 0 0 1 1 0 0 0 0 0 t 0 0 2 1 0 0 2 0 0 0 2 1 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_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_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; sssccvGCCCCGCCCCvGggCsss ; Alignment reference a 101 91 46 48 64 205 39 44 46 29 40 40 34 20 22 35 240 35 49 49 33 143 74 96 c 259 251 165 424 440 198 107 499 457 487 472 43 489 506 494 485 168 110 146 147 514 218 261 255 g 195 204 376 135 119 177 461 84 110 94 82 528 103 97 91 106 187 482 429 421 71 203 236 214 t 98 107 66 46 30 73 46 26 40 43 59 42 27 30 46 27 58 26 29 36 35 89 82 88

MA0079.3_shift6 (SP1) 0.887 0.406 3.477 0.405 0.935 1.033 0.953 4 37 16 23 8 6 6 14.286 13
; oligos_6nt_test_vs_ctrl_m5 versus MA0079.3 (SP1); m=1/2; ncol2=11; w=11; offset=6; strand=D; shift=6; score=14.2857; ------gCCCCkCCCCy------- ; cor=0.887; Ncor=0.406; logoDP=3.477; NIcor=0.405; NsEucl=0.935; SSD=1.033; NSW=0.953; rcor=4; rNcor=37; rlogoDP=16; rNIcor=23; rNsEucl=8; rSSD=6; rNSW=6; rank_mean=14.286; match_rank=13 a 0 0 0 0 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 0 0 0 c 0 0 0 0 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 0 0 0 g 0 0 0 0 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 0 0 0 t 0 0 0 0 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0 0 0 0

MA0516.1_shift6 (SP2) 0.781 0.488 3.445 0.477 0.932 2.107 0.930 30 28 17 20 13 36 23 23.857 26
; oligos_6nt_test_vs_ctrl_m5 versus MA0516.1 (SP2); m=2/2; ncol2=15; w=15; offset=6; strand=D; shift=6; score=23.8571; ------gyCCCGCCyCyyccs--- ; cor=0.781; Ncor=0.488; logoDP=3.445; NIcor=0.477; NsEucl=0.932; SSD=2.107; NSW=0.930; rcor=30; rNcor=28; rlogoDP=17; rNIcor=20; rNsEucl=13; rSSD=36; rNSW=23; rank_mean=23.857; match_rank=26 a 0 0 0 0 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 0 0 0 c 0 0 0 0 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 0 0 0 g 0 0 0 0 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 0 0 0 t 0 0 0 0 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316 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_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)																	; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=24; shift=0; ncol=24; sssccvGCCCCGCCCCvGggCsss ; Alignment reference a 101 91 46 48 64 205 39 44 46 29 40 40 34 20 22 35 240 35 49 49 33 143 74 96 c 259 251 165 424 440 198 107 499 457 487 472 43 489 506 494 485 168 110 146 147 514 218 261 255 g 195 204 376 135 119 177 461 84 110 94 82 528 103 97 91 106 187 482 429 421 71 203 236 214 t 98 107 66 46 30 73 46 26 40 43 59 42 27 30 46 27 58 26 29 36 35 89 82 88
MA0079.3_shift6 (SP1)	0.887	0.406	3.477	0.405	0.935	1.033	0.953	4	37	16	23	8	6	6	14.286	13	; oligos_6nt_test_vs_ctrl_m5 versus MA0079.3 (SP1); m=1/2; ncol2=11; w=11; offset=6; strand=D; shift=6; score=14.2857; ------gCCCCkCCCCy------- ; cor=0.887; Ncor=0.406; logoDP=3.477; NIcor=0.405; NsEucl=0.935; SSD=1.033; NSW=0.953; rcor=4; rNcor=37; rlogoDP=16; rNIcor=23; rNsEucl=8; rSSD=6; rNSW=6; rank_mean=14.286; match_rank=13 a 0 0 0 0 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 0 0 0 c 0 0 0 0 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 0 0 0 g 0 0 0 0 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 0 0 0 t 0 0 0 0 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0 0 0 0
MA0516.1_shift6 (SP2)	0.781	0.488	3.445	0.477	0.932	2.107	0.930	30	28	17	20	13	36	23	23.857	26	; oligos_6nt_test_vs_ctrl_m5 versus MA0516.1 (SP2); m=2/2; ncol2=15; w=15; offset=6; strand=D; shift=6; score=23.8571; ------gyCCCGCCyCyyccs--- ; cor=0.781; Ncor=0.488; logoDP=3.445; NIcor=0.477; NsEucl=0.932; SSD=2.107; NSW=0.930; rcor=30; rNcor=28; rlogoDP=17; rNIcor=20; rNsEucl=13; rSSD=36; rNSW=23; rank_mean=23.857; match_rank=26 a 0 0 0 0 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 0 0 0 c 0 0 0 0 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 0 0 0 g 0 0 0 0 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 0 0 0 t 0 0 0 0 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift3 ; 2 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ssAGGGAGCcg ; Alignment reference a 0 0 0 102 77 451 0 0 1 456 0 9 122 93 c 0 0 0 158 174 45 9 15 2 60 1 494 171 129 g 0 0 0 154 219 17 513 506 517 5 521 2 118 210 t 0 0 0 108 52 9 0 1 2 1 0 17 111 90

MA0154.1_shift0 (EBF1) 0.884 0.442 5.690 0.454 0.912 0.766 0.945 6 34 4 22 27 2 9 14.857 14
; oligos_6nt_test_vs_ctrl_m3 versus MA0154.1 (EBF1); m=1/1; ncol2=10; w=7; offset=-3; strand=D; shift=0; score=14.8571; mCyCmaGGGA---- ; cor=0.884; Ncor=0.442; logoDP=5.690; NIcor=0.454; NsEucl=0.912; SSD=0.766; NSW=0.945; rcor=6; rNcor=34; rlogoDP=4; rNIcor=22; rNsEucl=27; rSSD=2; rNSW=9; rank_mean=14.857; match_rank=14 a 11 0 1 2 11 16 0 2 0 21 0 0 0 0 c 9 22 16 20 9 1 0 0 0 0 0 0 0 0 g 2 0 1 0 0 5 25 23 25 4 0 0 0 0 t 3 3 7 3 5 3 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_test_vs_ctrl_m3_shift3 (oligos_6nt_test_vs_ctrl_m3)																		; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ssAGGGAGCcg ; Alignment reference a 0 0 0 102 77 451 0 0 1 456 0 9 122 93 c 0 0 0 158 174 45 9 15 2 60 1 494 171 129 g 0 0 0 154 219 17 513 506 517 5 521 2 118 210 t 0 0 0 108 52 9 0 1 2 1 0 17 111 90
MA0154.1_shift0 (EBF1)		0.884	0.442	5.690	0.454	0.912	0.766	0.945	6	34	4	22	27	2	9	14.857	14	; oligos_6nt_test_vs_ctrl_m3 versus MA0154.1 (EBF1); m=1/1; ncol2=10; w=7; offset=-3; strand=D; shift=0; score=14.8571; mCyCmaGGGA---- ; cor=0.884; Ncor=0.442; logoDP=5.690; NIcor=0.454; NsEucl=0.912; SSD=0.766; NSW=0.945; rcor=6; rNcor=34; rlogoDP=4; rNIcor=22; rNsEucl=27; rSSD=2; rNSW=9; rank_mean=14.857; match_rank=14 a 11 0 1 2 11 16 0 2 0 21 0 0 0 0 c 9 22 16 20 9 1 0 0 0 0 0 0 0 0 g 2 0 1 0 0 5 25 23 25 4 0 0 0 0 t 3 3 7 3 5 3 0 0 0 0 0 0 0 0

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

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=16; shift=0; ncol=21; sssgCCGCCCCGCCss----- ; Alignment reference a 178 210 115 69 64 74 71 36 50 53 76 63 80 71 162 161 0 0 0 0 0 c 601 517 356 308 1049 1061 98 1167 1019 1009 1028 156 951 976 568 541 0 0 0 0 0 g 423 471 827 929 201 178 1129 131 253 246 187 1082 266 251 448 481 0 0 0 0 0 t 176 180 80 72 64 65 80 44 56 70 87 77 81 80 200 195 0 0 0 0 0

MA0079.2_shift7 (SP1) 0.875 0.463 2.457 0.468 0.925 0.919 0.949 8 30 26 21 19 4 7 16.429 16
; oligos_6nt_test_vs_ctrl_m1 versus MA0079.2 (SP1); m=1/5; ncol2=10; w=9; offset=7; strand=D; shift=7; score=16.4286; -------CCCCkCCCCC---- ; cor=0.875; Ncor=0.463; logoDP=2.457; NIcor=0.468; NsEucl=0.925; SSD=0.919; NSW=0.949; rcor=8; rNcor=30; rlogoDP=26; rNIcor=21; rNsEucl=19; rSSD=4; rNSW=7; rank_mean=16.429; match_rank=16 a 0 0 0 0 0 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 0 0 0 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 0 0 0 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 0 0 0 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0

MA0516.1_shift6 (SP2) 0.856 0.408 2.853 0.401 0.921 1.242 0.938 12 35 23 24 20 11 17 20.286 18
; oligos_6nt_test_vs_ctrl_m1 versus MA0516.1 (SP2); m=2/5; ncol2=15; w=10; offset=6; strand=D; shift=6; score=20.2857; ------gyCCCGCCyCyyccs ; cor=0.856; Ncor=0.408; logoDP=2.853; NIcor=0.401; NsEucl=0.921; SSD=1.242; NSW=0.938; rcor=12; rNcor=35; rlogoDP=23; rNIcor=24; rNsEucl=20; rSSD=11; rNSW=17; rank_mean=20.286; match_rank=18 a 0 0 0 0 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 0 0 0 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 0 0 0 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 0 0 0 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316

MA0079.3_shift6 (SP1) 0.839 0.494 2.917 0.480 0.917 1.373 0.931 17 26 22 19 25 19 22 21.429 20
; oligos_6nt_test_vs_ctrl_m1 versus MA0079.3 (SP1); m=3/5; ncol2=11; w=10; offset=6; strand=D; shift=6; score=21.4286; ------gCCCCkCCCCy---- ; cor=0.839; Ncor=0.494; logoDP=2.917; NIcor=0.480; NsEucl=0.917; SSD=1.373; NSW=0.931; rcor=17; rNcor=26; rlogoDP=22; rNIcor=19; rNsEucl=25; rSSD=19; rNSW=22; rank_mean=21.429; match_rank=20 a 0 0 0 0 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 0 0 0 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 0 0 0 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 0 0 0 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0

MA0599.1_shift6 (KLF5) 0.817 0.510 2.976 0.498 0.912 1.544 0.923 23 22 19 15 26 21 28 22.000 21
; oligos_6nt_test_vs_ctrl_m1 versus MA0599.1 (KLF5); m=4/5; ncol2=10; w=10; offset=6; strand=D; shift=6; score= 22; ------gCCMCrCCCh----- ; cor=0.817; Ncor=0.510; logoDP=2.976; NIcor=0.498; NsEucl=0.912; SSD=1.544; NSW=0.923; rcor=23; rNcor=22; rlogoDP=19; rNIcor=15; rNsEucl=26; rSSD=21; rNSW=28; rank_mean=22.000; match_rank=21 a 0 0 0 0 0 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 0 0 0 0 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 0 0 0 0 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0

MA0039.2_rc_shift6 (Klf4_rc) 0.793 0.496 1.341 -0.002 0.907 1.743 0.913 28 25 30 30 33 28 31 29.286 32
; oligos_6nt_test_vs_ctrl_m1 versus MA0039.2_rc (Klf4_rc); m=5/5; ncol2=10; w=10; offset=6; strand=R; shift=6; score=29.2857; ------gCCmCrCCCw----- ; cor=0.793; Ncor=0.496; logoDP=1.341; NIcor=-0.002; NsEucl=0.907; SSD=1.743; NSW=0.913; rcor=28; rNcor=25; rlogoDP=30; rNIcor=30; rNsEucl=33; rSSD=28; rNSW=31; rank_mean=29.286; match_rank=32 a 0 0 0 0 0 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 0 0 0 0 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 0 0 0 0 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 0 0 0 0 0 254 123 264 42 22 277 14 14 88 1468 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_shift0 (oligos_6nt_test_vs_ctrl_m1)																	; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=16; shift=0; ncol=21; sssgCCGCCCCGCCss----- ; Alignment reference a 178 210 115 69 64 74 71 36 50 53 76 63 80 71 162 161 0 0 0 0 0 c 601 517 356 308 1049 1061 98 1167 1019 1009 1028 156 951 976 568 541 0 0 0 0 0 g 423 471 827 929 201 178 1129 131 253 246 187 1082 266 251 448 481 0 0 0 0 0 t 176 180 80 72 64 65 80 44 56 70 87 77 81 80 200 195 0 0 0 0 0
MA0079.2_shift7 (SP1)	0.875	0.463	2.457	0.468	0.925	0.919	0.949	8	30	26	21	19	4	7	16.429	16	; oligos_6nt_test_vs_ctrl_m1 versus MA0079.2 (SP1); m=1/5; ncol2=10; w=9; offset=7; strand=D; shift=7; score=16.4286; -------CCCCkCCCCC---- ; cor=0.875; Ncor=0.463; logoDP=2.457; NIcor=0.468; NsEucl=0.925; SSD=0.919; NSW=0.949; rcor=8; rNcor=30; rlogoDP=26; rNIcor=21; rNsEucl=19; rSSD=4; rNSW=7; rank_mean=16.429; match_rank=16 a 0 0 0 0 0 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 0 0 0 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 0 0 0 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 0 0 0 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0
MA0516.1_shift6 (SP2)	0.856	0.408	2.853	0.401	0.921	1.242	0.938	12	35	23	24	20	11	17	20.286	18	; oligos_6nt_test_vs_ctrl_m1 versus MA0516.1 (SP2); m=2/5; ncol2=15; w=10; offset=6; strand=D; shift=6; score=20.2857; ------gyCCCGCCyCyyccs ; cor=0.856; Ncor=0.408; logoDP=2.853; NIcor=0.401; NsEucl=0.921; SSD=1.242; NSW=0.938; rcor=12; rNcor=35; rlogoDP=23; rNIcor=24; rNsEucl=20; rSSD=11; rNSW=17; rank_mean=20.286; match_rank=18 a 0 0 0 0 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 0 0 0 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 0 0 0 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 0 0 0 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316
MA0079.3_shift6 (SP1)	0.839	0.494	2.917	0.480	0.917	1.373	0.931	17	26	22	19	25	19	22	21.429	20	; oligos_6nt_test_vs_ctrl_m1 versus MA0079.3 (SP1); m=3/5; ncol2=11; w=10; offset=6; strand=D; shift=6; score=21.4286; ------gCCCCkCCCCy---- ; cor=0.839; Ncor=0.494; logoDP=2.917; NIcor=0.480; NsEucl=0.917; SSD=1.373; NSW=0.931; rcor=17; rNcor=26; rlogoDP=22; rNIcor=19; rNsEucl=25; rSSD=19; rNSW=22; rank_mean=21.429; match_rank=20 a 0 0 0 0 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 0 0 0 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 0 0 0 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 0 0 0 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0
MA0599.1_shift6 (KLF5)	0.817	0.510	2.976	0.498	0.912	1.544	0.923	23	22	19	15	26	21	28	22.000	21	; oligos_6nt_test_vs_ctrl_m1 versus MA0599.1 (KLF5); m=4/5; ncol2=10; w=10; offset=6; strand=D; shift=6; score= 22; ------gCCMCrCCCh----- ; cor=0.817; Ncor=0.510; logoDP=2.976; NIcor=0.498; NsEucl=0.912; SSD=1.544; NSW=0.923; rcor=23; rNcor=22; rlogoDP=19; rNIcor=15; rNsEucl=26; rSSD=21; rNSW=28; rank_mean=22.000; match_rank=21 a 0 0 0 0 0 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 0 0 0 0 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 0 0 0 0 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0
MA0039.2_rc_shift6 (Klf4_rc)	0.793	0.496	1.341	-0.002	0.907	1.743	0.913	28	25	30	30	33	28	31	29.286	32	; oligos_6nt_test_vs_ctrl_m1 versus MA0039.2_rc (Klf4_rc); m=5/5; ncol2=10; w=10; offset=6; strand=R; shift=6; score=29.2857; ------gCCmCrCCCw----- ; cor=0.793; Ncor=0.496; logoDP=1.341; NIcor=-0.002; NsEucl=0.907; SSD=1.743; NSW=0.913; rcor=28; rNcor=25; rlogoDP=30; rNIcor=30; rNsEucl=33; rSSD=28; rNSW=31; rank_mean=29.286; match_rank=32 a 0 0 0 0 0 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 0 0 0 0 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 0 0 0 0 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 0 0 0 0 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_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_7nt_test_vs_ctrl_m5_shift4 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=12; shift=4; ncol=16; ----CrCACACACACr ; Alignment reference a 0 0 0 0 5 35 0 77 0 80 0 80 0 76 3 27 c 0 0 0 0 73 9 96 0 101 1 102 0 101 2 86 4 g 0 0 0 0 4 54 2 25 1 21 0 22 0 24 4 68 t 0 0 0 0 20 4 4 0 0 0 0 0 1 0 9 3

MA0472.1_shift0 (EGR2) 0.797 0.548 7.036 0.541 0.908 2.051 0.907 27 16 3 12 32 35 33 22.571 22
; oligos_7nt_test_vs_ctrl_m5 versus MA0472.1 (EGR2); m=1/2; ncol2=15; w=11; offset=-4; strand=D; shift=0; score=22.5714; cmcmCrCCCACrCac- ; cor=0.797; Ncor=0.548; logoDP=7.036; NIcor=0.541; NsEucl=0.908; SSD=2.051; NSW=0.907; rcor=27; rNcor=16; rlogoDP=3; rNIcor=12; rNsEucl=32; rSSD=35; rNSW=33; rank_mean=22.571; match_rank=22 a 169 337 168 387 26 448 0 152 0 1059 0 460 0 558 127 0 c 572 460 572 722 1186 0 1246 1094 1169 187 1246 0 1041 302 617 0 g 291 180 216 65 0 602 0 0 0 0 0 579 114 199 251 0 t 214 269 290 72 34 196 0 0 77 0 0 207 91 187 251 0

MA0006.1_rc_shift8 (Arnt::Ahr_rc) 0.813 0.407 2.375 -0.002 0.865 1.310 0.891 24 36 27 29 38 15 37 29.429 33
; oligos_7nt_test_vs_ctrl_m5 versus MA0006.1_rc (Arnt::Ahr_rc); m=2/2; ncol2=6; w=6; offset=4; strand=R; shift=8; score=29.4286; --------CACGCr-- ; cor=0.813; Ncor=0.407; logoDP=2.375; NIcor=-0.002; NsEucl=0.865; SSD=1.310; NSW=0.891; rcor=24; rNcor=36; rlogoDP=27; rNIcor=29; rNsEucl=38; rSSD=15; rNSW=37; rank_mean=29.429; match_rank=33 a 0 0 0 0 0 0 0 0 0 24 1 1 1 11 0 0 c 0 0 0 0 0 0 0 0 24 0 23 0 23 2 0 0 g 0 0 0 0 0 0 0 0 0 0 0 23 0 8 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 3 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_7nt_test_vs_ctrl_m5_shift4 (oligos_7nt_test_vs_ctrl_m5)																	; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=12; shift=4; ncol=16; ----CrCACACACACr ; Alignment reference a 0 0 0 0 5 35 0 77 0 80 0 80 0 76 3 27 c 0 0 0 0 73 9 96 0 101 1 102 0 101 2 86 4 g 0 0 0 0 4 54 2 25 1 21 0 22 0 24 4 68 t 0 0 0 0 20 4 4 0 0 0 0 0 1 0 9 3
MA0472.1_shift0 (EGR2)	0.797	0.548	7.036	0.541	0.908	2.051	0.907	27	16	3	12	32	35	33	22.571	22	; oligos_7nt_test_vs_ctrl_m5 versus MA0472.1 (EGR2); m=1/2; ncol2=15; w=11; offset=-4; strand=D; shift=0; score=22.5714; cmcmCrCCCACrCac- ; cor=0.797; Ncor=0.548; logoDP=7.036; NIcor=0.541; NsEucl=0.908; SSD=2.051; NSW=0.907; rcor=27; rNcor=16; rlogoDP=3; rNIcor=12; rNsEucl=32; rSSD=35; rNSW=33; rank_mean=22.571; match_rank=22 a 169 337 168 387 26 448 0 152 0 1059 0 460 0 558 127 0 c 572 460 572 722 1186 0 1246 1094 1169 187 1246 0 1041 302 617 0 g 291 180 216 65 0 602 0 0 0 0 0 579 114 199 251 0 t 214 269 290 72 34 196 0 0 77 0 0 207 91 187 251 0
MA0006.1_rc_shift8 (Arnt::Ahr_rc)	0.813	0.407	2.375	-0.002	0.865	1.310	0.891	24	36	27	29	38	15	37	29.429	33	; oligos_7nt_test_vs_ctrl_m5 versus MA0006.1_rc (Arnt::Ahr_rc); m=2/2; ncol2=6; w=6; offset=4; strand=R; shift=8; score=29.4286; --------CACGCr-- ; cor=0.813; Ncor=0.407; logoDP=2.375; NIcor=-0.002; NsEucl=0.865; SSD=1.310; NSW=0.891; rcor=24; rNcor=36; rlogoDP=27; rNIcor=29; rNsEucl=38; rSSD=15; rNSW=37; rank_mean=29.429; match_rank=33 a 0 0 0 0 0 0 0 0 0 24 1 1 1 11 0 0 c 0 0 0 0 0 0 0 0 24 0 23 0 23 2 0 0 g 0 0 0 0 0 0 0 0 0 0 0 23 0 8 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift0 ; 5 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
dyads_test_vs_ctrl_m1_shift0 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; ssCtGCCCtssGGCCaggGCCcsg ; Alignment reference a 40 26 6 29 1 5 7 3 16 23 50 7 5 11 11 82 13 19 8 14 8 13 28 34 c 76 82 141 38 18 173 169 191 43 70 54 26 28 166 167 50 49 32 26 153 145 139 68 50 g 57 64 46 36 172 20 22 13 28 110 94 169 163 18 16 51 137 138 157 26 35 33 77 91 t 34 35 14 104 16 9 9 0 120 4 9 5 11 12 13 24 8 18 16 14 19 22 34 32

MA0003.2_rc_shift3 (TFAP2A_rc) 0.818 0.511 0.828 -0.130 0.939 1.701 0.943 22 21 34 37 5 26 14 22.714 24
; dyads_test_vs_ctrl_m1 versus MA0003.2_rc (TFAP2A_rc); m=1/4; ncol2=15; w=15; offset=3; strand=R; shift=3; score=22.7143; ---tGsCCTsrGGCwrtk------ ; cor=0.818; Ncor=0.511; logoDP=0.828; NIcor=-0.130; NsEucl=0.939; SSD=1.701; NSW=0.943; rcor=22; rNcor=21; rlogoDP=34; rNIcor=37; rNsEucl=5; rSSD=26; rNSW=14; rank_mean=22.714; match_rank=24 a 0 0 0 1094 510 84 0 0 204 308 3215 336 0 131 2077 1981 1105 1230 0 0 0 0 0 0 c 0 0 0 168 465 3455 5098 4638 920 1715 85 0 0 3712 985 884 792 851 0 0 0 0 0 0 g 0 0 0 690 3672 1443 0 0 236 2729 1736 4762 5098 1199 519 1506 1060 1630 0 0 0 0 0 0 t 0 0 0 3146 451 116 0 460 3738 346 62 0 0 56 1517 727 2141 1387 0 0 0 0 0 0

MA0524.1_rc_shift3 (TFAP2C_rc) 0.809 0.506 0.734 -0.143 0.938 1.755 0.941 25 23 37 38 6 29 16 24.857 27
; dyads_test_vs_ctrl_m1 versus MA0524.1_rc (TFAP2C_rc); m=2/4; ncol2=15; w=15; offset=3; strand=R; shift=3; score=24.8571; ---tgsCCTGrGGshrkd------ ; cor=0.809; Ncor=0.506; logoDP=0.734; NIcor=-0.143; NsEucl=0.938; SSD=1.755; NSW=0.941; rcor=25; rNcor=23; rlogoDP=37; rNIcor=38; rNsEucl=6; rSSD=29; rNSW=16; rank_mean=24.857; match_rank=27 a 0 0 0 3726 3060 11 0 0 789 786 7872 3609 0 932 5401 8290 3909 4750 0 0 0 0 0 0 c 0 0 0 2536 1788 10222 18426 18235 1195 1768 1237 0 0 11033 6098 2643 3347 2123 0 0 0 0 0 0 g 0 0 0 3259 9235 7908 0 0 0 14790 9317 14817 18426 6040 2009 4943 4693 6752 0 0 0 0 0 0 t 0 0 0 8905 4343 285 0 191 16442 1082 0 0 0 421 4918 2550 6477 4801 0 0 0 0 0 0

MA0146.1_rc_shift9 (Zfx_rc) 0.770 0.449 2.691 0.383 0.928 2.012 0.928 33 31 25 25 15 31 25 26.429 28
; dyads_test_vs_ctrl_m1 versus MA0146.1_rc (Zfx_rc); m=3/4; ncol2=14; w=14; offset=9; strand=R; shift=9; score=26.4286; ---------sAGGCCbvGscsss- ; cor=0.770; Ncor=0.449; logoDP=2.691; NIcor=0.383; NsEucl=0.928; SSD=2.012; NSW=0.928; rcor=33; rNcor=31; rlogoDP=25; rNIcor=25; rNsEucl=15; rSSD=31; rNSW=25; rank_mean=26.429; match_rank=28 a 0 0 0 0 0 0 0 0 0 56 479 1 0 1 1 15 144 111 30 60 37 75 70 0 c 0 0 0 0 0 0 0 0 0 219 0 0 0 477 469 121 182 2 144 298 199 172 179 0 g 0 0 0 0 0 0 0 0 0 122 2 480 480 3 2 154 125 362 297 49 151 170 177 0 t 0 0 0 0 0 0 0 0 0 84 0 0 1 0 9 191 30 6 10 72 91 60 50 0

MA0146.2_rc_shift9 (Zfx_rc) 0.769 0.449 2.697 0.383 0.928 2.021 0.928 34 32 24 26 16 32 26 27.143 29
; dyads_test_vs_ctrl_m1 versus MA0146.2_rc (Zfx_rc); m=4/4; ncol2=14; w=14; offset=9; strand=R; shift=9; score=27.1429; ---------sAGGCCbvGscsss- ; cor=0.769; Ncor=0.449; logoDP=2.697; NIcor=0.383; NsEucl=0.928; SSD=2.021; NSW=0.928; rcor=34; rNcor=32; rlogoDP=24; rNIcor=26; rNsEucl=16; rSSD=32; rNSW=26; rank_mean=27.143; match_rank=29 a 0 0 0 0 0 0 0 0 0 56 480 1 0 1 1 15 144 112 30 61 37 75 70 0 c 0 0 0 0 0 0 0 0 0 218 0 0 0 477 470 122 183 2 144 297 199 173 179 0 g 0 0 0 0 0 0 0 0 0 122 1 480 481 3 2 153 124 361 297 49 151 170 178 0 t 0 0 0 0 0 0 0 0 0 84 0 0 0 0 8 191 30 6 10 72 91 59 50 0

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_m1_shift0 (dyads_test_vs_ctrl_m1)																	; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; ssCtGCCCtssGGCCaggGCCcsg ; Alignment reference a 40 26 6 29 1 5 7 3 16 23 50 7 5 11 11 82 13 19 8 14 8 13 28 34 c 76 82 141 38 18 173 169 191 43 70 54 26 28 166 167 50 49 32 26 153 145 139 68 50 g 57 64 46 36 172 20 22 13 28 110 94 169 163 18 16 51 137 138 157 26 35 33 77 91 t 34 35 14 104 16 9 9 0 120 4 9 5 11 12 13 24 8 18 16 14 19 22 34 32
MA0003.2_rc_shift3 (TFAP2A_rc)	0.818	0.511	0.828	-0.130	0.939	1.701	0.943	22	21	34	37	5	26	14	22.714	24	; dyads_test_vs_ctrl_m1 versus MA0003.2_rc (TFAP2A_rc); m=1/4; ncol2=15; w=15; offset=3; strand=R; shift=3; score=22.7143; ---tGsCCTsrGGCwrtk------ ; cor=0.818; Ncor=0.511; logoDP=0.828; NIcor=-0.130; NsEucl=0.939; SSD=1.701; NSW=0.943; rcor=22; rNcor=21; rlogoDP=34; rNIcor=37; rNsEucl=5; rSSD=26; rNSW=14; rank_mean=22.714; match_rank=24 a 0 0 0 1094 510 84 0 0 204 308 3215 336 0 131 2077 1981 1105 1230 0 0 0 0 0 0 c 0 0 0 168 465 3455 5098 4638 920 1715 85 0 0 3712 985 884 792 851 0 0 0 0 0 0 g 0 0 0 690 3672 1443 0 0 236 2729 1736 4762 5098 1199 519 1506 1060 1630 0 0 0 0 0 0 t 0 0 0 3146 451 116 0 460 3738 346 62 0 0 56 1517 727 2141 1387 0 0 0 0 0 0
MA0524.1_rc_shift3 (TFAP2C_rc)	0.809	0.506	0.734	-0.143	0.938	1.755	0.941	25	23	37	38	6	29	16	24.857	27	; dyads_test_vs_ctrl_m1 versus MA0524.1_rc (TFAP2C_rc); m=2/4; ncol2=15; w=15; offset=3; strand=R; shift=3; score=24.8571; ---tgsCCTGrGGshrkd------ ; cor=0.809; Ncor=0.506; logoDP=0.734; NIcor=-0.143; NsEucl=0.938; SSD=1.755; NSW=0.941; rcor=25; rNcor=23; rlogoDP=37; rNIcor=38; rNsEucl=6; rSSD=29; rNSW=16; rank_mean=24.857; match_rank=27 a 0 0 0 3726 3060 11 0 0 789 786 7872 3609 0 932 5401 8290 3909 4750 0 0 0 0 0 0 c 0 0 0 2536 1788 10222 18426 18235 1195 1768 1237 0 0 11033 6098 2643 3347 2123 0 0 0 0 0 0 g 0 0 0 3259 9235 7908 0 0 0 14790 9317 14817 18426 6040 2009 4943 4693 6752 0 0 0 0 0 0 t 0 0 0 8905 4343 285 0 191 16442 1082 0 0 0 421 4918 2550 6477 4801 0 0 0 0 0 0
MA0146.1_rc_shift9 (Zfx_rc)	0.770	0.449	2.691	0.383	0.928	2.012	0.928	33	31	25	25	15	31	25	26.429	28	; dyads_test_vs_ctrl_m1 versus MA0146.1_rc (Zfx_rc); m=3/4; ncol2=14; w=14; offset=9; strand=R; shift=9; score=26.4286; ---------sAGGCCbvGscsss- ; cor=0.770; Ncor=0.449; logoDP=2.691; NIcor=0.383; NsEucl=0.928; SSD=2.012; NSW=0.928; rcor=33; rNcor=31; rlogoDP=25; rNIcor=25; rNsEucl=15; rSSD=31; rNSW=25; rank_mean=26.429; match_rank=28 a 0 0 0 0 0 0 0 0 0 56 479 1 0 1 1 15 144 111 30 60 37 75 70 0 c 0 0 0 0 0 0 0 0 0 219 0 0 0 477 469 121 182 2 144 298 199 172 179 0 g 0 0 0 0 0 0 0 0 0 122 2 480 480 3 2 154 125 362 297 49 151 170 177 0 t 0 0 0 0 0 0 0 0 0 84 0 0 1 0 9 191 30 6 10 72 91 60 50 0
MA0146.2_rc_shift9 (Zfx_rc)	0.769	0.449	2.697	0.383	0.928	2.021	0.928	34	32	24	26	16	32	26	27.143	29	; dyads_test_vs_ctrl_m1 versus MA0146.2_rc (Zfx_rc); m=4/4; ncol2=14; w=14; offset=9; strand=R; shift=9; score=27.1429; ---------sAGGCCbvGscsss- ; cor=0.769; Ncor=0.449; logoDP=2.697; NIcor=0.383; NsEucl=0.928; SSD=2.021; NSW=0.928; rcor=34; rNcor=32; rlogoDP=24; rNIcor=26; rNsEucl=16; rSSD=32; rNSW=26; rank_mean=27.143; match_rank=29 a 0 0 0 0 0 0 0 0 0 56 480 1 0 1 1 15 144 112 30 61 37 75 70 0 c 0 0 0 0 0 0 0 0 0 218 0 0 0 477 470 122 183 2 144 297 199 173 179 0 g 0 0 0 0 0 0 0 0 0 122 1 480 481 3 2 153 124 361 297 49 151 170 178 0 t 0 0 0 0 0 0 0 0 0 84 0 0 0 0 8 191 30 6 10 72 91 59 50 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
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=24; sssssscgCGCCCCGCCCvsssss ; Alignment reference a 153 137 120 109 106 88 107 81 62 81 55 67 55 60 59 61 55 35 327 68 105 94 162 157 c 514 510 621 396 680 723 734 305 887 202 918 840 880 853 158 886 882 934 392 311 313 340 535 476 g 386 435 329 600 332 316 276 744 207 850 190 239 239 218 941 226 244 200 376 776 732 699 373 418 t 171 142 154 119 106 97 107 94 68 91 61 78 50 93 66 51 43 55 129 69 74 91 154 173

MA0516.1_shift9 (SP2) 0.772 0.482 2.970 0.488 0.933 2.046 0.932 31 29 20 16 10 34 21 23.000 25
; oligos_6nt_test_vs_ctrl_m4 versus MA0516.1 (SP2); m=1/1; ncol2=15; w=15; offset=9; strand=D; shift=9; score= 23; ---------gyCCCGCCyCyyccs ; cor=0.772; Ncor=0.482; logoDP=2.970; NIcor=0.488; NsEucl=0.933; SSD=2.046; NSW=0.932; rcor=31; rNcor=29; rlogoDP=20; rNIcor=16; rNsEucl=10; rSSD=34; rNSW=21; rank_mean=23.000; match_rank=25 a 0 0 0 0 0 0 0 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 0 0 0 0 0 0 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 0 0 0 0 0 0 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 0 0 0 0 0 0 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316

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=24; sssssscgCGCCCCGCCCvsssss ; Alignment reference a 153 137 120 109 106 88 107 81 62 81 55 67 55 60 59 61 55 35 327 68 105 94 162 157 c 514 510 621 396 680 723 734 305 887 202 918 840 880 853 158 886 882 934 392 311 313 340 535 476 g 386 435 329 600 332 316 276 744 207 850 190 239 239 218 941 226 244 200 376 776 732 699 373 418 t 171 142 154 119 106 97 107 94 68 91 61 78 50 93 66 51 43 55 129 69 74 91 154 173
MA0516.1_shift9 (SP2)		0.772	0.482	2.970	0.488	0.933	2.046	0.932	31	29	20	16	10	34	21	23.000	25	; oligos_6nt_test_vs_ctrl_m4 versus MA0516.1 (SP2); m=1/1; ncol2=15; w=15; offset=9; strand=D; shift=9; score= 23; ---------gyCCCGCCyCyyccs ; cor=0.772; Ncor=0.482; logoDP=2.970; NIcor=0.488; NsEucl=0.933; SSD=2.046; NSW=0.932; rcor=31; rNcor=29; rlogoDP=20; rNIcor=16; rNsEucl=10; rSSD=34; rNSW=21; rank_mean=23.000; match_rank=25 a 0 0 0 0 0 0 0 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 0 0 0 0 0 0 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 0 0 0 0 0 0 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 0 0 0 0 0 0 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift6 ; 5 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift6 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=12; shift=6; ncol=18; ------ssGmGGGmGGcG ; Alignment reference a 0 0 0 0 0 0 9 5 1 45 0 1 1 50 0 1 7 4 c 0 0 0 0 0 0 39 46 8 24 12 12 0 26 6 1 51 6 g 0 0 0 0 0 0 22 23 66 6 63 63 75 0 70 73 10 52 t 0 0 0 0 0 0 6 2 1 1 1 0 0 0 0 1 8 14

MA0162.2_rc_shift5 (EGR1_rc) 0.761 0.652 0.942 -0.120 0.910 2.332 0.903 37 9 33 35 28 38 35 30.714 34
; oligos_7nt_test_vs_ctrl_m4 versus MA0162.2_rc (EGR1_rc); m=1/4; ncol2=14; w=12; offset=-1; strand=R; shift=5; score=30.7143; -----gGmGKGGGcGGgg ; cor=0.761; Ncor=0.652; logoDP=0.942; NIcor=-0.120; NsEucl=0.910; SSD=2.332; NSW=0.903; rcor=37; rNcor=9; rlogoDP=33; rNIcor=35; rNsEucl=28; rSSD=38; rNSW=35; rank_mean=30.714; match_rank=34 a 0 0 0 0 0 1722 987 3289 304 243 1491 404 0 2505 449 490 2797 2544 c 0 0 0 0 0 1913 1420 6599 0 0 611 0 0 6840 0 0 2250 1359 g 0 0 0 0 0 5595 9849 0 11952 8361 10154 11852 12256 0 11574 10431 6049 6847 t 0 0 0 0 0 3026 0 2368 0 3652 0 0 0 2911 233 1335 1160 1506

MA0469.1_rc_shift0 (E2F3_rc) 0.807 0.403 0.591 0.030 0.897 1.705 0.905 26 38 38 28 35 27 34 32.286 36
; oligos_7nt_test_vs_ctrl_m4 versus MA0469.1_rc (E2F3_rc); m=2/4; ncol2=15; w=9; offset=-6; strand=R; shift=0; score=32.2857; srsygsggGCGGGAr--- ; cor=0.807; Ncor=0.403; logoDP=0.591; NIcor=0.030; NsEucl=0.897; SSD=1.705; NSW=0.905; rcor=26; rNcor=38; rlogoDP=38; rNIcor=28; rNsEucl=35; rSSD=27; rNSW=34; rank_mean=32.286; match_rank=36 a 259 645 160 274 302 629 460 239 0 309 0 0 0 2549 1149 0 0 0 c 644 200 582 512 556 742 397 607 0 2240 0 80 0 0 0 0 0 0 g 718 640 1075 329 1495 903 1327 1703 2549 0 2549 2469 2549 0 1400 0 0 0 t 305 441 109 811 196 275 365 0 0 0 0 0 0 0 0 0 0 0

MA0599.1_rc_shift9 (KLF5_rc) 0.762 0.528 1.176 -0.082 0.888 2.022 0.888 36 18 31 34 37 33 38 32.429 37
; oligos_7nt_test_vs_ctrl_m4 versus MA0599.1_rc (KLF5_rc); m=3/4; ncol2=10; w=9; offset=3; strand=R; shift=9; score=32.4286; ---------dGGGyGKGG ; cor=0.762; Ncor=0.528; logoDP=1.176; NIcor=-0.082; NsEucl=0.888; SSD=2.022; NSW=0.888; rcor=36; rNcor=18; rlogoDP=31; rNIcor=34; rNsEucl=37; rSSD=33; rNSW=38; rank_mean=32.429; match_rank=37 a 0 0 0 0 0 0 0 0 0 4101 476 0 0 3378 0 565 1603 1711 c 0 0 0 0 0 0 0 0 0 0 0 0 0 5182 0 0 0 0 g 0 0 0 0 0 0 0 0 0 5595 13135 13611 13611 0 13611 9569 12008 11900 t 0 0 0 0 0 0 0 0 0 3915 0 0 0 5051 0 3477 0 0

MA0079.3_rc_shift8 (SP1_rc) 0.764 0.588 0.789 -0.121 0.896 2.158 0.892 35 14 35 36 36 37 36 32.714 38
; oligos_7nt_test_vs_ctrl_m4 versus MA0079.3_rc (SP1_rc); m=4/4; ncol2=11; w=10; offset=2; strand=R; shift=8; score=32.7143; --------rGGGGmGGGG ; cor=0.764; Ncor=0.588; logoDP=0.789; NIcor=-0.121; NsEucl=0.896; SSD=2.158; NSW=0.892; rcor=35; rNcor=14; rlogoDP=35; rNIcor=36; rNsEucl=36; rSSD=37; rNSW=36; rank_mean=32.714; match_rank=38 a 0 0 0 0 0 0 0 0 2379 1323 2055 0 0 2751 73 0 1932 1877 c 0 0 0 0 0 0 0 0 734 0 0 0 0 4624 0 0 0 642 g 0 0 0 0 0 0 0 0 4969 6357 6679 8734 8734 0 8661 8734 6703 6215 t 0 0 0 0 0 0 0 0 652 1054 0 0 0 1359 0 0 99 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_test_vs_ctrl_m4_shift6 (oligos_7nt_test_vs_ctrl_m4)																	; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=12; shift=6; ncol=18; ------ssGmGGGmGGcG ; Alignment reference a 0 0 0 0 0 0 9 5 1 45 0 1 1 50 0 1 7 4 c 0 0 0 0 0 0 39 46 8 24 12 12 0 26 6 1 51 6 g 0 0 0 0 0 0 22 23 66 6 63 63 75 0 70 73 10 52 t 0 0 0 0 0 0 6 2 1 1 1 0 0 0 0 1 8 14
MA0162.2_rc_shift5 (EGR1_rc)	0.761	0.652	0.942	-0.120	0.910	2.332	0.903	37	9	33	35	28	38	35	30.714	34	; oligos_7nt_test_vs_ctrl_m4 versus MA0162.2_rc (EGR1_rc); m=1/4; ncol2=14; w=12; offset=-1; strand=R; shift=5; score=30.7143; -----gGmGKGGGcGGgg ; cor=0.761; Ncor=0.652; logoDP=0.942; NIcor=-0.120; NsEucl=0.910; SSD=2.332; NSW=0.903; rcor=37; rNcor=9; rlogoDP=33; rNIcor=35; rNsEucl=28; rSSD=38; rNSW=35; rank_mean=30.714; match_rank=34 a 0 0 0 0 0 1722 987 3289 304 243 1491 404 0 2505 449 490 2797 2544 c 0 0 0 0 0 1913 1420 6599 0 0 611 0 0 6840 0 0 2250 1359 g 0 0 0 0 0 5595 9849 0 11952 8361 10154 11852 12256 0 11574 10431 6049 6847 t 0 0 0 0 0 3026 0 2368 0 3652 0 0 0 2911 233 1335 1160 1506
MA0469.1_rc_shift0 (E2F3_rc)	0.807	0.403	0.591	0.030	0.897	1.705	0.905	26	38	38	28	35	27	34	32.286	36	; oligos_7nt_test_vs_ctrl_m4 versus MA0469.1_rc (E2F3_rc); m=2/4; ncol2=15; w=9; offset=-6; strand=R; shift=0; score=32.2857; srsygsggGCGGGAr--- ; cor=0.807; Ncor=0.403; logoDP=0.591; NIcor=0.030; NsEucl=0.897; SSD=1.705; NSW=0.905; rcor=26; rNcor=38; rlogoDP=38; rNIcor=28; rNsEucl=35; rSSD=27; rNSW=34; rank_mean=32.286; match_rank=36 a 259 645 160 274 302 629 460 239 0 309 0 0 0 2549 1149 0 0 0 c 644 200 582 512 556 742 397 607 0 2240 0 80 0 0 0 0 0 0 g 718 640 1075 329 1495 903 1327 1703 2549 0 2549 2469 2549 0 1400 0 0 0 t 305 441 109 811 196 275 365 0 0 0 0 0 0 0 0 0 0 0
MA0599.1_rc_shift9 (KLF5_rc)	0.762	0.528	1.176	-0.082	0.888	2.022	0.888	36	18	31	34	37	33	38	32.429	37	; oligos_7nt_test_vs_ctrl_m4 versus MA0599.1_rc (KLF5_rc); m=3/4; ncol2=10; w=9; offset=3; strand=R; shift=9; score=32.4286; ---------dGGGyGKGG ; cor=0.762; Ncor=0.528; logoDP=1.176; NIcor=-0.082; NsEucl=0.888; SSD=2.022; NSW=0.888; rcor=36; rNcor=18; rlogoDP=31; rNIcor=34; rNsEucl=37; rSSD=33; rNSW=38; rank_mean=32.429; match_rank=37 a 0 0 0 0 0 0 0 0 0 4101 476 0 0 3378 0 565 1603 1711 c 0 0 0 0 0 0 0 0 0 0 0 0 0 5182 0 0 0 0 g 0 0 0 0 0 0 0 0 0 5595 13135 13611 13611 0 13611 9569 12008 11900 t 0 0 0 0 0 0 0 0 0 3915 0 0 0 5051 0 3477 0 0
MA0079.3_rc_shift8 (SP1_rc)	0.764	0.588	0.789	-0.121	0.896	2.158	0.892	35	14	35	36	36	37	36	32.714	38	; oligos_7nt_test_vs_ctrl_m4 versus MA0079.3_rc (SP1_rc); m=4/4; ncol2=11; w=10; offset=2; strand=R; shift=8; score=32.7143; --------rGGGGmGGGG ; cor=0.764; Ncor=0.588; logoDP=0.789; NIcor=-0.121; NsEucl=0.896; SSD=2.158; NSW=0.892; rcor=35; rNcor=14; rlogoDP=35; rNIcor=36; rNsEucl=36; rSSD=37; rNSW=36; rank_mean=32.714; match_rank=38 a 0 0 0 0 0 0 0 0 2379 1323 2055 0 0 2751 73 0 1932 1877 c 0 0 0 0 0 0 0 0 734 0 0 0 0 4624 0 0 0 642 g 0 0 0 0 0 0 0 0 4969 6357 6679 8734 8734 0 8661 8734 6703 6215 t 0 0 0 0 0 0 0 0 652 1054 0 0 0 1359 0 0 99 0