One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift3 ; 9 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)																		; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=3; ncol=17; ---wrTTACACAAya-- ; Alignment reference a 0 0 0 701 1073 23 1 2580 0 2542 0 2578 2579 307 920 0 0 c 0 0 0 409 457 6 0 0 2580 0 2580 0 1 755 634 0 0 g 0 0 0 616 697 30 0 0 0 38 0 2 0 388 415 0 0 t 0 0 0 854 353 2521 2579 0 0 0 0 0 0 1130 611 0 0
oligos_8nt_mkv6_m4_shift3 (oligos_8nt_mkv6_m4)		0.985	0.909	13.429	0.906	0.975	0.179	0.993	1	4	12	2	1	1	1	3.143	1	; oligos_7nt_mkv5_m3 versus oligos_8nt_mkv6_m4; m=1/8; ncol2=13; w=12; offset=0; strand=D; shift=3; score= 3.1429; ---wrTTACACAATah- ; cor=0.985; Ncor=0.909; logoDP=13.429; NIcor=0.906; NsEucl=0.975; SSD=0.179; NSW=0.993; rcor=1; rNcor=4; rlogoDP=12; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=3.143; match_rank=1 a 0 0 0 768 1278 9 3 2545 2 2026 1 2529 2545 143 934 674 0 c 0 0 0 372 377 3 0 0 2552 7 2516 4 1 447 595 648 0 g 0 0 0 562 670 8 10 10 2 516 0 21 8 179 403 433 0 t 0 0 0 862 239 2544 2551 9 8 15 47 10 10 1795 632 809 0
oligos_8nt_mkv6_m2_rc_shift2 (oligos_8nt_mkv6_m2_rc)		0.849	0.727	7.189	0.337	0.920	1.853	0.923	37	56	85	86	46	29	38	53.857	50	; oligos_7nt_mkv5_m3 versus oligos_8nt_mkv6_m2_rc; m=2/8; ncol2=14; w=12; offset=-1; strand=R; shift=2; score=53.8571; --wtATTTCACAATmw- ; cor=0.849; Ncor=0.727; logoDP=7.189; NIcor=0.337; NsEucl=0.920; SSD=1.853; NSW=0.923; rcor=37; rNcor=56; rlogoDP=85; rNIcor=86; rNsEucl=46; rSSD=29; rNSW=38; rank_mean=53.857; match_rank=50 a 0 0 1173 770 3364 10 29 427 24 3664 23 3968 3993 167 1554 1082 0 c 0 0 786 669 246 7 6 11 3990 36 3924 32 8 569 1034 987 0 g 0 0 869 982 333 6 63 359 2 263 14 9 10 238 553 658 0 t 0 0 1207 1614 92 4012 3937 3238 19 72 74 26 24 3061 894 1308 0
positions_7nt_m1_shift2 (positions_7nt_m1)		0.804	0.643	11.321	0.620	0.906	2.557	0.893	67	86	51	61	89	64	80	71.143	75	; oligos_7nt_mkv5_m3 versus positions_7nt_m1; m=3/8; ncol2=15; w=12; offset=-1; strand=D; shift=2; score=71.1429; --wtATTTCACAATCwy ; cor=0.804; Ncor=0.643; logoDP=11.321; NIcor=0.620; NsEucl=0.906; SSD=2.557; NSW=0.893; rcor=67; rNcor=86; rlogoDP=51; rNIcor=61; rNsEucl=89; rSSD=64; rNSW=80; rank_mean=71.143; match_rank=75 a 0 0 394 218 1344 6 10 132 6 1281 17 1366 1387 18 237 486 348 c 0 0 277 242 17 9 7 9 1392 26 1335 33 4 63 1048 300 369 g 0 0 313 341 33 4 46 166 3 48 5 1 6 13 43 155 231 t 0 0 419 602 9 1384 1340 1096 2 48 46 3 6 1309 75 462 455
oligos_8nt_mkv6_m1_shift1 (oligos_8nt_mkv6_m1)		0.787	0.630	11.896	0.624	0.902	2.754	0.885	81	93	37	57	94	75	86	74.714	80	; oligos_7nt_mkv5_m3 versus oligos_8nt_mkv6_m1; m=4/8; ncol2=15; w=12; offset=-2; strand=D; shift=1; score=74.7143; -atGGTTGCACAATah- ; cor=0.787; Ncor=0.630; logoDP=11.896; NIcor=0.624; NsEucl=0.902; SSD=2.754; NSW=0.885; rcor=81; rNcor=93; rlogoDP=37; rNIcor=57; rNsEucl=94; rSSD=75; rNSW=86; rank_mean=74.714; match_rank=80 a 0 916 519 193 371 2 4 54 1 2146 57 2247 2242 18 885 631 0 c 0 427 233 24 77 4 0 3 2252 32 2134 18 4 475 510 578 0 g 0 477 406 1804 1760 2 8 2128 5 32 14 0 14 49 354 370 0 t 0 447 1109 246 59 2259 2255 82 9 57 62 2 7 1725 518 688 0
positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)		0.815	0.652	1.974	-0.067	0.910	2.320	0.903	59	83	101	101	80	51	64	77.000	84	; oligos_7nt_mkv5_m3 versus positions_6nt_m1_rc; m=5/8; ncol2=15; w=12; offset=0; strand=R; shift=3; score= 77; ---kaTTTCACAATCTw ; cor=0.815; Ncor=0.652; logoDP=1.974; NIcor=-0.067; NsEucl=0.910; SSD=2.320; NSW=0.903; rcor=59; rNcor=83; rlogoDP=101; rNIcor=101; rNsEucl=80; rSSD=51; rNSW=64; rank_mean=77.000; match_rank=84 a 0 0 0 188 538 7 10 87 4 820 5 866 880 4 132 75 243 c 0 0 0 107 114 14 5 6 885 7 850 17 3 16 695 31 215 g 0 0 0 239 182 2 31 79 1 40 2 2 5 8 23 19 176 t 0 0 0 359 59 870 847 721 3 26 36 8 5 865 43 768 259
positions_6nt_m2_shift2 (positions_6nt_m2)		0.770	0.616	10.681	0.588	0.899	2.917	0.878	92	101	63	73	103	87	102	88.714	102	; oligos_7nt_mkv5_m3 versus positions_6nt_m2; m=6/8; ncol2=15; w=12; offset=-1; strand=D; shift=2; score=88.7143; --dkATTACGCAAGArw ; cor=0.770; Ncor=0.616; logoDP=10.681; NIcor=0.588; NsEucl=0.899; SSD=2.917; NSW=0.878; rcor=92; rNcor=101; rlogoDP=63; rNIcor=73; rNsEucl=103; rSSD=87; rNSW=102; rank_mean=88.714; match_rank=102 a 0 0 201 156 603 2 1 580 30 65 11 668 668 9 620 178 200 c 0 0 107 113 23 2 2 3 534 20 638 1 0 57 15 145 138 g 0 0 172 198 33 1 11 48 28 569 1 0 1 531 14 185 143 t 0 0 189 202 10 664 655 38 77 15 19 0 0 72 20 161 188
positions_8nt_m4_shift0 (positions_8nt_m4)		0.751	0.530	12.649	0.516	0.889	3.518	0.853	110	108	29	77	111	106	111	93.143	104	; oligos_7nt_mkv5_m3 versus positions_8nt_m4; m=7/8; ncol2=17; w=12; offset=-3; strand=D; shift=0; score=93.1429; raTGGTTGCACAAyAwt ; cor=0.751; Ncor=0.530; logoDP=12.649; NIcor=0.516; NsEucl=0.889; SSD=3.518; NSW=0.853; rcor=110; rNcor=108; rlogoDP=29; rNIcor=77; rNsEucl=111; rSSD=106; rNSW=111; rank_mean=93.143; match_rank=104 a 176 350 19 19 55 1 1 11 1 634 4 646 645 6 548 174 92 c 61 81 8 2 8 0 0 2 643 3 635 1 0 239 29 149 112 g 352 112 19 612 578 0 0 628 0 5 1 0 0 12 34 147 50 t 58 104 601 14 6 646 646 6 3 5 7 0 2 390 36 177 393
positions_8nt_m2_rc_shift2 (positions_8nt_m2_rc)		0.771	0.578	0.307	-0.198	0.898	3.001	0.875	91	105	109	108	105	89	104	101.571	108	; oligos_7nt_mkv5_m3 versus positions_8nt_m2_rc; m=8/8; ncol2=16; w=12; offset=-1; strand=R; shift=2; score=101.571; --htcTTGCACAATCAy ; cor=0.771; Ncor=0.578; logoDP=0.307; NIcor=-0.198; NsEucl=0.898; SSD=3.001; NSW=0.875; rcor=91; rNcor=105; rlogoDP=109; rNIcor=108; rNsEucl=105; rSSD=89; rNSW=104; rank_mean=101.571; match_rank=108 a 0 0 160 131 141 2 0 25 4 601 17 626 629 13 23 558 156 c 0 0 165 107 406 4 0 3 632 7 594 10 1 24 576 24 178 g 0 0 147 129 72 0 4 586 1 12 4 1 4 12 20 13 131 t 0 0 166 271 19 632 634 24 1 18 23 1 4 589 19 43 173

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift1 ; 16 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5)																		; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=15; shift=1; ncol=18; -atGATTGCACAACwy-- ; Alignment reference a 0 1046 663 145 2141 1 1 72 6 2545 94 2687 2687 42 1152 677 0 0 c 0 471 240 158 56 4 1 6 2698 51 2522 26 10 2208 613 803 0 0 g 0 578 483 2160 474 4 10 2428 2 31 16 1 9 95 166 539 0 0 t 0 620 1329 252 44 2706 2703 209 9 88 83 1 9 370 784 696 0 0
oligos_7nt_mkv5_m1_shift2 (oligos_7nt_mkv5_m1)		0.968	0.904	13.030	0.896	0.967	0.431	0.985	3	6	19	3	3	3	3	5.714	2	; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m1; m=1/15; ncol2=14; w=14; offset=1; strand=D; shift=2; score= 5.7143; --wkATTGCACAAywh-- ; cor=0.968; Ncor=0.904; logoDP=13.030; NIcor=0.896; NsEucl=0.967; SSD=0.431; NSW=0.985; rcor=3; rNcor=6; rlogoDP=19; rNIcor=3; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=5.714; match_rank=2 a 0 0 1173 857 3161 3 5 52 3 4369 17 4506 4512 149 1831 1226 0 0 c 0 0 816 719 307 3 4 3 4509 16 4467 9 3 2623 988 1193 0 0 g 0 0 861 1532 915 4 3 4418 2 107 5 4 3 337 502 930 0 0 t 0 0 1671 1413 138 4511 4509 48 7 29 32 2 3 1412 1200 1172 0 0
positions_7nt_m2_shift0 (positions_7nt_m2)		0.941	0.830	13.434	0.823	0.954	0.933	0.969	10	21	11	12	10	11	10	12.143	7	; oligos_6nt_mkv4_m5 versus positions_7nt_m2; m=2/15; ncol2=17; w=15; offset=-1; strand=D; shift=0; score=12.1429; rmAGATTGCACAACTyt- ; cor=0.941; Ncor=0.830; logoDP=13.434; NIcor=0.823; NsEucl=0.954; SSD=0.933; NSW=0.969; rcor=10; rNcor=21; rlogoDP=11; rNIcor=12; rNsEucl=10; rSSD=11; rNSW=10; rank_mean=12.143; match_rank=7 a 94 132 260 16 314 0 0 10 2 311 7 331 333 6 35 67 73 0 c 71 85 4 10 5 0 0 0 330 11 318 3 0 296 15 105 76 0 g 95 77 9 277 13 1 2 309 1 1 1 0 0 7 2 77 54 0 t 74 40 61 31 2 333 332 15 1 11 8 0 1 25 282 85 131 0
oligos_8nt_mkv6_m1_shift1 (oligos_8nt_mkv6_m1)		0.889	0.889	12.492	0.867	0.942	1.537	0.949	21	8	31	4	18	22	20	17.714	10	; oligos_6nt_mkv4_m5 versus oligos_8nt_mkv6_m1; m=3/15; ncol2=15; w=15; offset=0; strand=D; shift=1; score=17.7143; -atGGTTGCACAATah-- ; cor=0.889; Ncor=0.889; logoDP=12.492; NIcor=0.867; NsEucl=0.942; SSD=1.537; NSW=0.949; rcor=21; rNcor=8; rlogoDP=31; rNIcor=4; rNsEucl=18; rSSD=22; rNSW=20; rank_mean=17.714; match_rank=10 a 0 916 519 193 371 2 4 54 1 2146 57 2247 2242 18 885 631 0 0 c 0 427 233 24 77 4 0 3 2252 32 2134 18 4 475 510 578 0 0 g 0 477 406 1804 1760 2 8 2128 5 32 14 0 14 49 354 370 0 0 t 0 447 1109 246 59 2259 2255 82 9 57 62 2 7 1725 518 688 0 0
positions_8nt_m4_shift0 (positions_8nt_m4)		0.872	0.769	13.664	0.741	0.933	2.047	0.932	25	32	7	26	28	37	31	26.571	18	; oligos_6nt_mkv4_m5 versus positions_8nt_m4; m=4/15; ncol2=17; w=15; offset=-1; strand=D; shift=0; score=26.5714; raTGGTTGCACAAyAwt- ; cor=0.872; Ncor=0.769; logoDP=13.664; NIcor=0.741; NsEucl=0.933; SSD=2.047; NSW=0.932; rcor=25; rNcor=32; rlogoDP=7; rNIcor=26; rNsEucl=28; rSSD=37; rNSW=31; rank_mean=26.571; match_rank=18 a 176 350 19 19 55 1 1 11 1 634 4 646 645 6 548 174 92 0 c 61 81 8 2 8 0 0 2 643 3 635 1 0 239 29 149 112 0 g 352 112 19 612 578 0 0 628 0 5 1 0 0 12 34 147 50 0 t 58 104 601 14 6 646 646 6 3 5 7 0 2 390 36 177 393 0
positions_8nt_m1_shift0 (positions_8nt_m1)		0.863	0.810	11.722	0.797	0.934	1.952	0.935	30	26	43	16	26	32	28	28.714	23	; oligos_6nt_mkv4_m5 versus positions_8nt_m1; m=5/15; ncol2=16; w=15; offset=-1; strand=D; shift=0; score=28.7143; amAGATTGCAAAACww-- ; cor=0.863; Ncor=0.810; logoDP=11.722; NIcor=0.797; NsEucl=0.934; SSD=1.952; NSW=0.935; rcor=30; rNcor=26; rlogoDP=43; rNIcor=16; rNsEucl=26; rSSD=32; rNSW=28; rank_mean=28.714; match_rank=23 a 172 182 482 52 497 2 2 12 3 517 451 522 535 8 215 163 0 0 c 112 161 5 27 15 3 0 2 539 6 70 25 3 479 124 119 0 0 g 134 132 23 439 22 2 2 518 5 15 2 2 7 22 43 128 0 0 t 131 74 39 31 15 542 545 17 2 11 26 0 4 40 167 139 0 0
positions_7nt_m5_shift0 (positions_7nt_m5)		0.864	0.762	13.204	0.760	0.932	2.081	0.931	29	37	16	23	29	39	32	29.286	24	; oligos_6nt_mkv4_m5 versus positions_7nt_m5; m=6/15; ncol2=17; w=15; offset=-1; strand=D; shift=0; score=29.2857; wmACATTGCACAACTsy- ; cor=0.864; Ncor=0.762; logoDP=13.204; NIcor=0.760; NsEucl=0.932; SSD=2.081; NSW=0.931; rcor=29; rNcor=37; rlogoDP=16; rNIcor=23; rNsEucl=29; rSSD=39; rNSW=32; rank_mean=29.286; match_rank=24 a 73 84 193 16 219 0 0 4 0 221 11 226 224 2 20 52 44 0 c 48 64 6 163 4 0 0 0 227 3 213 1 0 205 12 64 62 0 g 45 44 16 18 0 0 3 206 0 1 1 0 1 4 0 58 48 0 t 62 36 13 31 5 228 225 18 1 3 3 1 3 17 196 54 74 0
positions_8nt_m3_shift2 (positions_8nt_m3)		0.787	0.734	11.870	0.736	0.915	2.825	0.899	82	54	38	30	69	80	70	60.429	59	; oligos_6nt_mkv4_m5 versus positions_8nt_m3; m=7/15; ncol2=14; w=14; offset=1; strand=D; shift=2; score=60.4286; --wtATTGCCCAATaw-- ; cor=0.787; Ncor=0.734; logoDP=11.870; NIcor=0.736; NsEucl=0.915; SSD=2.825; NSW=0.899; rcor=82; rNcor=54; rlogoDP=38; rNIcor=30; rNsEucl=69; rSSD=80; rNSW=70; rank_mean=60.429; match_rank=59 a 0 0 331 246 842 1 1 12 2 34 5 1110 1118 50 412 284 0 0 c 0 0 229 210 94 0 1 0 1116 933 1097 4 0 179 259 273 0 0 g 0 0 247 258 141 0 1 1104 0 142 4 3 0 80 183 202 0 0 t 0 0 311 404 41 1117 1115 2 0 9 12 1 0 809 264 359 0 0
oligos_8nt_mkv6_m2_rc_shift2 (oligos_8nt_mkv6_m2_rc)		0.807	0.753	8.485	0.474	0.919	2.544	0.909	65	44	82	83	47	61	55	62.429	61	; oligos_6nt_mkv4_m5 versus oligos_8nt_mkv6_m2_rc; m=8/15; ncol2=14; w=14; offset=1; strand=R; shift=2; score=62.4286; --wtATTTCACAATmw-- ; cor=0.807; Ncor=0.753; logoDP=8.485; NIcor=0.474; NsEucl=0.919; SSD=2.544; NSW=0.909; rcor=65; rNcor=44; rlogoDP=82; rNIcor=83; rNsEucl=47; rSSD=61; rNSW=55; rank_mean=62.429; match_rank=61 a 0 0 1173 770 3364 10 29 427 24 3664 23 3968 3993 167 1554 1082 0 0 c 0 0 786 669 246 7 6 11 3990 36 3924 32 8 569 1034 987 0 0 g 0 0 869 982 333 6 63 359 2 263 14 9 10 238 553 658 0 0 t 0 0 1207 1614 92 4012 3937 3238 19 72 74 26 24 3061 894 1308 0 0
oligos_8nt_mkv6_m3_rc_shift2 (oligos_8nt_mkv6_m3_rc)		0.803	0.750	9.466	0.599	0.919	2.587	0.908	68	46	77	70	51	67	60	62.714	62	; oligos_6nt_mkv4_m5 versus oligos_8nt_mkv6_m3_rc; m=9/15; ncol2=14; w=14; offset=1; strand=R; shift=2; score=62.7143; --wtATTGCTCAATaw-- ; cor=0.803; Ncor=0.750; logoDP=9.466; NIcor=0.599; NsEucl=0.919; SSD=2.587; NSW=0.908; rcor=68; rNcor=46; rlogoDP=77; rNIcor=70; rNsEucl=51; rSSD=67; rNSW=60; rank_mean=62.714; match_rank=62 a 0 0 955 726 2742 8 7 108 16 677 97 3295 3306 83 1479 930 0 0 c 0 0 676 534 213 4 4 6 3305 96 3053 20 9 325 682 791 0 0 g 0 0 749 657 291 9 10 3149 10 210 9 5 6 180 505 573 0 0 t 0 0 955 1418 89 3314 3314 72 4 2352 176 15 14 2747 669 1041 0 0
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)		0.785	0.628	11.776	0.622	0.902	2.781	0.884	83	94	42	59	95	76	87	76.571	83	; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m3; m=10/15; ncol2=12; w=12; offset=2; strand=D; shift=3; score=76.5714; ---wrTTACACAAya--- ; cor=0.785; Ncor=0.628; logoDP=11.776; NIcor=0.622; NsEucl=0.902; SSD=2.781; NSW=0.884; rcor=83; rNcor=94; rlogoDP=42; rNIcor=59; rNsEucl=95; rSSD=76; rNSW=87; rank_mean=76.571; match_rank=83 a 0 0 0 701 1073 23 1 2580 0 2542 0 2578 2579 307 920 0 0 0 c 0 0 0 409 457 6 0 0 2580 0 2580 0 1 755 634 0 0 0 g 0 0 0 616 697 30 0 0 0 38 0 2 0 388 415 0 0 0 t 0 0 0 854 353 2521 2579 0 0 0 0 0 0 1130 611 0 0 0
oligos_7nt_mkv5_m5_shift3 (oligos_7nt_mkv5_m5)		0.779	0.624	11.920	0.614	0.900	2.861	0.881	87	97	36	66	99	82	93	80.000	90	; oligos_6nt_mkv4_m5 versus oligos_7nt_mkv5_m5; m=11/15; ncol2=12; w=12; offset=2; strand=D; shift=3; score= 80; ---wrTTGCTCAAya--- ; cor=0.779; Ncor=0.624; logoDP=11.920; NIcor=0.614; NsEucl=0.900; SSD=2.861; NSW=0.881; rcor=87; rNcor=97; rlogoDP=36; rNIcor=66; rNsEucl=99; rSSD=82; rNSW=93; rank_mean=80.000; match_rank=90 a 0 0 0 790 1154 0 0 0 0 5 0 2774 2774 284 977 0 0 0 c 0 0 0 474 551 0 1 0 2774 0 2774 0 0 848 665 0 0 0 g 0 0 0 595 751 0 0 2774 0 6 0 0 0 483 459 0 0 0 t 0 0 0 915 318 2774 2773 0 0 2763 0 0 0 1159 673 0 0 0
positions_7nt_m1_shift2 (positions_7nt_m1)		0.760	0.665	11.276	0.646	0.908	3.301	0.882	103	80	52	53	82	102	91	80.429	91	; oligos_6nt_mkv4_m5 versus positions_7nt_m1; m=12/15; ncol2=15; w=14; offset=1; strand=D; shift=2; score=80.4286; --wtATTTCACAATCwy- ; cor=0.760; Ncor=0.665; logoDP=11.276; NIcor=0.646; NsEucl=0.908; SSD=3.301; NSW=0.882; rcor=103; rNcor=80; rlogoDP=52; rNIcor=53; rNsEucl=82; rSSD=102; rNSW=91; rank_mean=80.429; match_rank=91 a 0 0 394 218 1344 6 10 132 6 1281 17 1366 1387 18 237 486 348 0 c 0 0 277 242 17 9 7 9 1392 26 1335 33 4 63 1048 300 369 0 g 0 0 313 341 33 4 46 166 3 48 5 1 6 13 43 155 231 0 t 0 0 419 602 9 1384 1340 1096 2 48 46 3 6 1309 75 462 455 0
positions_6nt_m4_shift0 (positions_6nt_m4)		0.762	0.635	12.834	0.627	0.908	3.821	0.873	100	89	27	56	84	108	106	81.429	94	; oligos_6nt_mkv4_m5 versus positions_6nt_m4; m=13/15; ncol2=18; w=15; offset=-1; strand=D; shift=0; score=81.4286; wsATGTTGCACAACAGtr ; cor=0.762; Ncor=0.635; logoDP=12.834; NIcor=0.627; NsEucl=0.908; SSD=3.821; NSW=0.873; rcor=100; rNcor=89; rlogoDP=27; rNIcor=56; rNsEucl=84; rSSD=108; rNSW=106; rank_mean=81.429; match_rank=94 a 39 29 88 5 6 0 1 4 2 115 3 118 117 2 106 5 21 32 c 22 32 16 1 4 0 0 0 114 0 110 0 0 110 2 8 25 29 g 27 31 7 0 106 0 0 110 1 0 1 0 0 3 2 99 25 33 t 30 26 7 112 2 118 117 4 1 3 4 0 1 3 8 6 47 24
oligos_8nt_mkv6_m5_shift3 (oligos_8nt_mkv6_m5)		0.774	0.619	11.830	0.618	0.899	2.911	0.879	90	100	39	63	102	86	100	82.857	95	; oligos_6nt_mkv4_m5 versus oligos_8nt_mkv6_m5; m=14/15; ncol2=12; w=12; offset=2; strand=D; shift=3; score=82.8571; ---waTTGCCCAAya--- ; cor=0.774; Ncor=0.619; logoDP=11.830; NIcor=0.618; NsEucl=0.899; SSD=2.911; NSW=0.879; rcor=90; rNcor=100; rlogoDP=39; rNIcor=63; rNsEucl=102; rSSD=86; rNSW=100; rank_mean=82.857; match_rank=95 a 0 0 0 519 683 0 0 0 0 5 0 1878 1880 230 606 0 0 0 c 0 0 0 405 470 0 0 0 1881 1825 1880 0 1 573 394 0 0 0 g 0 0 0 401 453 0 0 1879 0 50 0 3 0 432 449 0 0 0 t 0 0 0 556 275 1881 1881 2 0 1 1 0 0 646 432 0 0 0
oligos_8nt_mkv6_m4_shift3 (oligos_8nt_mkv6_m4)		0.757	0.656	10.944	0.651	0.904	3.118	0.880	106	82	60	52	91	96	95	83.143	97	; oligos_6nt_mkv4_m5 versus oligos_8nt_mkv6_m4; m=15/15; ncol2=13; w=13; offset=2; strand=D; shift=3; score=83.1429; ---wrTTACACAATah-- ; cor=0.757; Ncor=0.656; logoDP=10.944; NIcor=0.651; NsEucl=0.904; SSD=3.118; NSW=0.880; rcor=106; rNcor=82; rlogoDP=60; rNIcor=52; rNsEucl=91; rSSD=96; rNSW=95; rank_mean=83.143; match_rank=97 a 0 0 0 768 1278 9 3 2545 2 2026 1 2529 2545 143 934 674 0 0 c 0 0 0 372 377 3 0 0 2552 7 2516 4 1 447 595 648 0 0 g 0 0 0 562 670 8 10 10 2 516 0 21 8 179 403 433 0 0 t 0 0 0 862 239 2544 2551 9 8 15 47 10 10 1795 632 809 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m1_shift1 ; 12 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_8nt_mkv6_m1_shift1 (oligos_8nt_mkv6_m1)																		; oligos_8nt_mkv6_m1; m=0 (reference); ncol1=15; shift=1; ncol=18; -atGGTTGCACAATah-- ; Alignment reference a 0 916 519 193 371 2 4 54 1 2146 57 2247 2242 18 885 631 0 0 c 0 427 233 24 77 4 0 3 2252 32 2134 18 4 475 510 578 0 0 g 0 477 406 1804 1760 2 8 2128 5 32 14 0 14 49 354 370 0 0 t 0 447 1109 246 59 2259 2255 82 9 57 62 2 7 1725 518 688 0 0
positions_8nt_m4_shift0 (positions_8nt_m4)		0.961	0.848	14.340	0.834	0.961	0.687	0.977	5	13	3	8	5	7	6	6.714	3	; oligos_8nt_mkv6_m1 versus positions_8nt_m4; m=1/11; ncol2=17; w=15; offset=-1; strand=D; shift=0; score= 6.7143; raTGGTTGCACAAyAwt- ; cor=0.961; Ncor=0.848; logoDP=14.340; NIcor=0.834; NsEucl=0.961; SSD=0.687; NSW=0.977; rcor=5; rNcor=13; rlogoDP=3; rNIcor=8; rNsEucl=5; rSSD=7; rNSW=6; rank_mean=6.714; match_rank=3 a 176 350 19 19 55 1 1 11 1 634 4 646 645 6 548 174 92 0 c 61 81 8 2 8 0 0 2 643 3 635 1 0 239 29 149 112 0 g 352 112 19 612 578 0 0 628 0 5 1 0 0 12 34 147 50 0 t 58 104 601 14 6 646 646 6 3 5 7 0 2 390 36 177 393 0
oligos_8nt_mkv6_m3_rc_shift2 (oligos_8nt_mkv6_m3_rc)		0.809	0.755	9.654	0.604	0.920	2.507	0.910	62	41	76	68	45	60	51	57.571	53	; oligos_8nt_mkv6_m1 versus oligos_8nt_mkv6_m3_rc; m=2/11; ncol2=14; w=14; offset=1; strand=R; shift=2; score=57.5714; --wtATTGCTCAATaw-- ; cor=0.809; Ncor=0.755; logoDP=9.654; NIcor=0.604; NsEucl=0.920; SSD=2.507; NSW=0.910; rcor=62; rNcor=41; rlogoDP=76; rNIcor=68; rNsEucl=45; rSSD=60; rNSW=51; rank_mean=57.571; match_rank=53 a 0 0 955 726 2742 8 7 108 16 677 97 3295 3306 83 1479 930 0 0 c 0 0 676 534 213 4 4 6 3305 96 3053 20 9 325 682 791 0 0 g 0 0 749 657 291 9 10 3149 10 210 9 5 6 180 505 573 0 0 t 0 0 955 1418 89 3314 3314 72 4 2352 176 15 14 2747 669 1041 0 0
positions_8nt_m3_shift2 (positions_8nt_m3)		0.788	0.736	12.094	0.739	0.915	2.808	0.900	79	52	35	27	67	78	68	58.000	54	; oligos_8nt_mkv6_m1 versus positions_8nt_m3; m=3/11; ncol2=14; w=14; offset=1; strand=D; shift=2; score= 58; --wtATTGCCCAATaw-- ; cor=0.788; Ncor=0.736; logoDP=12.094; NIcor=0.739; NsEucl=0.915; SSD=2.808; NSW=0.900; rcor=79; rNcor=52; rlogoDP=35; rNIcor=27; rNsEucl=67; rSSD=78; rNSW=68; rank_mean=58.000; match_rank=54 a 0 0 331 246 842 1 1 12 2 34 5 1110 1118 50 412 284 0 0 c 0 0 229 210 94 0 1 0 1116 933 1097 4 0 179 259 273 0 0 g 0 0 247 258 141 0 1 1104 0 142 4 3 0 80 183 202 0 0 t 0 0 311 404 41 1117 1115 2 0 9 12 1 0 809 264 359 0 0
positions_7nt_m2_shift0 (positions_7nt_m2)		0.799	0.705	12.843	0.682	0.918	3.051	0.898	69	70	26	43	55	91	71	60.714	60	; oligos_8nt_mkv6_m1 versus positions_7nt_m2; m=4/11; ncol2=17; w=15; offset=-1; strand=D; shift=0; score=60.7143; rmAGATTGCACAACTyt- ; cor=0.799; Ncor=0.705; logoDP=12.843; NIcor=0.682; NsEucl=0.918; SSD=3.051; NSW=0.898; rcor=69; rNcor=70; rlogoDP=26; rNIcor=43; rNsEucl=55; rSSD=91; rNSW=71; rank_mean=60.714; match_rank=60 a 94 132 260 16 314 0 0 10 2 311 7 331 333 6 35 67 73 0 c 71 85 4 10 5 0 0 0 330 11 318 3 0 296 15 105 76 0 g 95 77 9 277 13 1 2 309 1 1 1 0 0 7 2 77 54 0 t 74 40 61 31 2 333 332 15 1 11 8 0 1 25 282 85 131 0
oligos_8nt_mkv6_m4_shift3 (oligos_8nt_mkv6_m4)		0.788	0.683	11.121	0.679	0.910	2.730	0.895	80	75	57	44	81	72	79	69.714	72	; oligos_8nt_mkv6_m1 versus oligos_8nt_mkv6_m4; m=5/11; ncol2=13; w=13; offset=2; strand=D; shift=3; score=69.7143; ---wrTTACACAATah-- ; cor=0.788; Ncor=0.683; logoDP=11.121; NIcor=0.679; NsEucl=0.910; SSD=2.730; NSW=0.895; rcor=80; rNcor=75; rlogoDP=57; rNIcor=44; rNsEucl=81; rSSD=72; rNSW=79; rank_mean=69.714; match_rank=72 a 0 0 0 768 1278 9 3 2545 2 2026 1 2529 2545 143 934 674 0 0 c 0 0 0 372 377 3 0 0 2552 7 2516 4 1 447 595 648 0 0 g 0 0 0 562 670 8 10 10 2 516 0 21 8 179 403 433 0 0 t 0 0 0 862 239 2544 2551 9 8 15 47 10 10 1795 632 809 0 0
oligos_8nt_mkv6_m2_rc_shift2 (oligos_8nt_mkv6_m2_rc)		0.792	0.739	8.757	0.490	0.916	2.738	0.902	75	51	81	81	63	73	65	69.857	73	; oligos_8nt_mkv6_m1 versus oligos_8nt_mkv6_m2_rc; m=6/11; ncol2=14; w=14; offset=1; strand=R; shift=2; score=69.8571; --wtATTTCACAATmw-- ; cor=0.792; Ncor=0.739; logoDP=8.757; NIcor=0.490; NsEucl=0.916; SSD=2.738; NSW=0.902; rcor=75; rNcor=51; rlogoDP=81; rNIcor=81; rNsEucl=63; rSSD=73; rNSW=65; rank_mean=69.857; match_rank=73 a 0 0 1173 770 3364 10 29 427 24 3664 23 3968 3993 167 1554 1082 0 0 c 0 0 786 669 246 7 6 11 3990 36 3924 32 8 569 1034 987 0 0 g 0 0 869 982 333 6 63 359 2 263 14 9 10 238 553 658 0 0 t 0 0 1207 1614 92 4012 3937 3238 19 72 74 26 24 3061 894 1308 0 0
positions_8nt_m2_rc_shift2 (positions_8nt_m2_rc)		0.822	0.677	0.390	-0.200	0.919	2.554	0.909	53	77	107	109	48	63	57	73.429	78	; oligos_8nt_mkv6_m1 versus positions_8nt_m2_rc; m=7/11; ncol2=16; w=14; offset=1; strand=R; shift=2; score=73.4286; --htcTTGCACAATCAyw ; cor=0.822; Ncor=0.677; logoDP=0.390; NIcor=-0.200; NsEucl=0.919; SSD=2.554; NSW=0.909; rcor=53; rNcor=77; rlogoDP=107; rNIcor=109; rNsEucl=48; rSSD=63; rNSW=57; rank_mean=73.429; match_rank=78 a 0 0 160 131 141 2 0 25 4 601 17 626 629 13 23 558 156 171 c 0 0 165 107 406 4 0 3 632 7 594 10 1 24 576 24 178 140 g 0 0 147 129 72 0 4 586 1 12 4 1 4 12 20 13 131 144 t 0 0 166 271 19 632 634 24 1 18 23 1 4 589 19 43 173 183
oligos_8nt_mkv6_m5_shift3 (oligos_8nt_mkv6_m5)		0.774	0.619	12.115	0.621	0.900	2.908	0.879	89	99	34	60	101	84	99	80.857	92	; oligos_8nt_mkv6_m1 versus oligos_8nt_mkv6_m5; m=8/11; ncol2=12; w=12; offset=2; strand=D; shift=3; score=80.8571; ---waTTGCCCAAya--- ; cor=0.774; Ncor=0.619; logoDP=12.115; NIcor=0.621; NsEucl=0.900; SSD=2.908; NSW=0.879; rcor=89; rNcor=99; rlogoDP=34; rNIcor=60; rNsEucl=101; rSSD=84; rNSW=99; rank_mean=80.857; match_rank=92 a 0 0 0 519 683 0 0 0 0 5 0 1878 1880 230 606 0 0 0 c 0 0 0 405 470 0 0 0 1881 1825 1880 0 1 573 394 0 0 0 g 0 0 0 401 453 0 0 1879 0 50 0 3 0 432 449 0 0 0 t 0 0 0 556 275 1881 1881 2 0 1 1 0 0 646 432 0 0 0
positions_7nt_m1_shift2 (positions_7nt_m1)		0.756	0.662	11.254	0.643	0.907	3.361	0.880	107	81	53	54	86	104	97	83.143	96	; oligos_8nt_mkv6_m1 versus positions_7nt_m1; m=9/11; ncol2=15; w=14; offset=1; strand=D; shift=2; score=83.1429; --wtATTTCACAATCwy- ; cor=0.756; Ncor=0.662; logoDP=11.254; NIcor=0.643; NsEucl=0.907; SSD=3.361; NSW=0.880; rcor=107; rNcor=81; rlogoDP=53; rNIcor=54; rNsEucl=86; rSSD=104; rNSW=97; rank_mean=83.143; match_rank=96 a 0 0 394 218 1344 6 10 132 6 1281 17 1366 1387 18 237 486 348 0 c 0 0 277 242 17 9 7 9 1392 26 1335 33 4 63 1048 300 369 0 g 0 0 313 341 33 4 46 166 3 48 5 1 6 13 43 155 231 0 t 0 0 419 602 9 1384 1340 1096 2 48 46 3 6 1309 75 462 455 0
positions_6nt_m4_shift0 (positions_6nt_m4)		0.757	0.631	12.940	0.623	0.907	3.896	0.870	105	92	22	58	87	109	109	83.143	98	; oligos_8nt_mkv6_m1 versus positions_6nt_m4; m=10/11; ncol2=18; w=15; offset=-1; strand=D; shift=0; score=83.1429; wsATGTTGCACAACAGtr ; cor=0.757; Ncor=0.631; logoDP=12.940; NIcor=0.623; NsEucl=0.907; SSD=3.896; NSW=0.870; rcor=105; rNcor=92; rlogoDP=22; rNIcor=58; rNsEucl=87; rSSD=109; rNSW=109; rank_mean=83.143; match_rank=98 a 39 29 88 5 6 0 1 4 2 115 3 118 117 2 106 5 21 32 c 22 32 16 1 4 0 0 0 114 0 110 0 0 110 2 8 25 29 g 27 31 7 0 106 0 0 110 1 0 1 0 0 3 2 99 25 33 t 30 26 7 112 2 118 117 4 1 3 4 0 1 3 8 6 47 24
positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)		0.770	0.589	0.518	-0.193	0.903	3.164	0.878	93	104	104	105	93	100	103	100.286	107	; oligos_8nt_mkv6_m1 versus positions_6nt_m1_rc; m=11/11; ncol2=15; w=13; offset=2; strand=R; shift=3; score=100.286; ---kaTTTCACAATCTww ; cor=0.770; Ncor=0.589; logoDP=0.518; NIcor=-0.193; NsEucl=0.903; SSD=3.164; NSW=0.878; rcor=93; rNcor=104; rlogoDP=104; rNIcor=105; rNsEucl=93; rSSD=100; rNSW=103; rank_mean=100.286; match_rank=107 a 0 0 0 188 538 7 10 87 4 820 5 866 880 4 132 75 243 237 c 0 0 0 107 114 14 5 6 885 7 850 17 3 16 695 31 215 172 g 0 0 0 239 182 2 31 79 1 40 2 2 5 8 23 19 176 127 t 0 0 0 359 59 870 847 721 3 26 36 8 5 865 43 768 259 357

One-to-n matrix alignment; reference matrix: positions_7nt_m2_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
positions_7nt_m2_shift0 (positions_7nt_m2)																		; positions_7nt_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; rmAGATTGCACAACTyt ; Alignment reference a 94 132 260 16 314 0 0 10 2 311 7 331 333 6 35 67 73 c 71 85 4 10 5 0 0 0 330 11 318 3 0 296 15 105 76 g 95 77 9 277 13 1 2 309 1 1 1 0 0 7 2 77 54 t 74 40 61 31 2 333 332 15 1 11 8 0 1 25 282 85 131
positions_7nt_m5_shift0 (positions_7nt_m5)		0.933	0.933	14.988	0.942	0.956	1.094	0.968	12	1	2	1	8	14	11	7.000	4	; positions_7nt_m2 versus positions_7nt_m5; m=1/3; ncol2=17; w=17; offset=0; strand=D; shift=0; score= 7; wmACATTGCACAACTsy ; cor=0.933; Ncor=0.933; logoDP=14.988; NIcor=0.942; NsEucl=0.956; SSD=1.094; NSW=0.968; rcor=12; rNcor=1; rlogoDP=2; rNIcor=1; rNsEucl=8; rSSD=14; rNSW=11; rank_mean=7.000; match_rank=4 a 73 84 193 16 219 0 0 4 0 221 11 226 224 2 20 52 44 c 48 64 6 163 4 0 0 0 227 3 213 1 0 205 12 64 62 g 45 44 16 18 0 0 3 206 0 1 1 0 1 4 0 58 48 t 62 36 13 31 5 228 225 18 1 3 3 1 3 17 196 54 74
positions_8nt_m1_shift0 (positions_8nt_m1)		0.885	0.833	12.909	0.823	0.941	1.797	0.944	24	19	24	13	20	28	23	21.571	12	; positions_7nt_m2 versus positions_8nt_m1; m=2/3; ncol2=16; w=16; offset=0; strand=D; shift=0; score=21.5714; amAGATTGCAAAACww- ; cor=0.885; Ncor=0.833; logoDP=12.909; NIcor=0.823; NsEucl=0.941; SSD=1.797; NSW=0.944; rcor=24; rNcor=19; rlogoDP=24; rNIcor=13; rNsEucl=20; rSSD=28; rNSW=23; rank_mean=21.571; match_rank=12 a 172 182 482 52 497 2 2 12 3 517 451 522 535 8 215 163 0 c 112 161 5 27 15 3 0 2 539 6 70 25 3 479 124 119 0 g 134 132 23 439 22 2 2 518 5 15 2 2 7 22 43 128 0 t 131 74 39 31 15 542 545 17 2 11 26 0 4 40 167 139 0
positions_7nt_m4_shift0 (positions_7nt_m4)		0.755	0.755	13.405	0.772	0.917	3.993	0.883	108	42	13	19	61	110	90	63.286	63	; positions_7nt_m2 versus positions_7nt_m4; m=3/3; ncol2=17; w=17; offset=0; strand=D; shift=0; score=63.2857; wyCTCTTGCACAACTbh ; cor=0.755; Ncor=0.755; logoDP=13.405; NIcor=0.772; NsEucl=0.917; SSD=3.993; NSW=0.883; rcor=108; rNcor=42; rlogoDP=13; rNIcor=19; rNsEucl=61; rSSD=110; rNSW=90; rank_mean=63.286; match_rank=63 a 53 47 13 1 20 0 1 2 0 180 11 195 197 3 6 36 50 c 42 60 160 8 160 0 0 0 198 8 185 2 1 178 15 53 54 g 45 38 9 0 18 0 1 189 1 3 1 1 0 3 3 54 24 t 59 54 17 190 1 199 197 8 0 8 2 1 1 15 175 56 71

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m5_shift1 ; 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_8nt_mkv6_m5_shift1 (oligos_8nt_mkv6_m5)																		; oligos_8nt_mkv6_m5; m=0 (reference); ncol1=12; shift=1; ncol=16; -waTTGCCCAAya--- ; Alignment reference a 0 519 683 0 0 0 0 5 0 1878 1880 230 606 0 0 0 c 0 405 470 0 0 0 1881 1825 1880 0 1 573 394 0 0 0 g 0 401 453 0 0 1879 0 50 0 3 0 432 449 0 0 0 t 0 556 275 1881 1881 2 0 1 1 0 0 646 432 0 0 0
positions_8nt_m3_shift0 (positions_8nt_m3)		0.964	0.826	13.802	0.821	0.961	0.448	0.981	4	23	6	14	6	4	4	8.714	5	; oligos_8nt_mkv6_m5 versus positions_8nt_m3; m=1/2; ncol2=14; w=12; offset=-1; strand=D; shift=0; score= 8.7143; wtATTGCCCAATaw-- ; cor=0.964; Ncor=0.826; logoDP=13.802; NIcor=0.821; NsEucl=0.961; SSD=0.448; NSW=0.981; rcor=4; rNcor=23; rlogoDP=6; rNIcor=14; rNsEucl=6; rSSD=4; rNSW=4; rank_mean=8.714; match_rank=5 a 331 246 842 1 1 12 2 34 5 1110 1118 50 412 284 0 0 c 229 210 94 0 1 0 1116 933 1097 4 0 179 259 273 0 0 g 247 258 141 0 1 1104 0 142 4 3 0 80 183 202 0 0 t 311 404 41 1117 1115 2 0 9 12 1 0 809 264 359 0 0
positions_8nt_m2_rc_shift0 (positions_8nt_m2_rc)		0.758	0.568	0.239	-0.195	0.895	3.152	0.869	104	107	111	107	107	99	110	106.429	111	; oligos_8nt_mkv6_m5 versus positions_8nt_m2_rc; m=2/2; ncol2=16; w=12; offset=-1; strand=R; shift=0; score=106.429; htcTTGCACAATCAyw ; cor=0.758; Ncor=0.568; logoDP=0.239; NIcor=-0.195; NsEucl=0.895; SSD=3.152; NSW=0.869; rcor=104; rNcor=107; rlogoDP=111; rNIcor=107; rNsEucl=107; rSSD=99; rNSW=110; rank_mean=106.429; match_rank=111 a 160 131 141 2 0 25 4 601 17 626 629 13 23 558 156 171 c 165 107 406 4 0 3 632 7 594 10 1 24 576 24 178 140 g 147 129 72 0 4 586 1 12 4 1 4 12 20 13 131 144 t 166 271 19 632 634 24 1 18 23 1 4 589 19 43 173 183

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m2_shift0 (dyads_m2)																		; dyads_m2; m=0 (reference); ncol1=17; shift=0; ncol=18; taAWTAAATAAATAAAw- ; Alignment reference a 169 428 683 502 27 709 718 719 19 722 721 719 5 714 717 592 306 0 c 112 46 25 9 9 3 3 1 2 1 1 1 6 1 0 22 54 0 g 29 179 5 25 3 5 2 4 4 0 2 3 0 5 3 52 41 0 t 415 72 12 189 686 8 2 1 700 2 1 2 714 5 5 59 324 0
dyads_m4_shift2 (dyads_m4)		0.959	0.799	16.555	0.785	0.959	0.765	0.974	6	29	1	17	7	8	7	10.714	6	; dyads_m2 versus dyads_m4; m=1/1; ncol2=16; w=15; offset=2; strand=D; shift=2; score=10.7143; --awyAAATAAATAAAww ; cor=0.959; Ncor=0.799; logoDP=16.555; NIcor=0.785; NsEucl=0.959; SSD=0.765; NSW=0.974; rcor=6; rNcor=29; rlogoDP=1; rNIcor=17; rNsEucl=7; rSSD=8; rNSW=7; rank_mean=10.714; match_rank=6 a 0 0 816 878 261 1523 1525 1523 37 1539 1545 1536 17 1531 1527 1524 565 769 c 0 0 357 125 635 13 8 9 27 9 9 8 28 11 20 10 156 222 g 0 0 180 136 26 10 26 21 21 13 8 19 16 16 8 12 105 130 t 0 0 214 428 645 21 8 14 1482 6 5 4 1506 9 12 21 741 446

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift2 ; 18 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_mkv5_m1_shift2 (oligos_7nt_mkv5_m1)																		; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=14; shift=2; ncol=18; --wkATTGCACAAywh-- ; Alignment reference a 0 0 1173 857 3161 3 5 52 3 4369 17 4506 4512 149 1831 1226 0 0 c 0 0 816 719 307 3 4 3 4509 16 4467 9 3 2623 988 1193 0 0 g 0 0 861 1532 915 4 3 4418 2 107 5 4 3 337 502 930 0 0 t 0 0 1671 1413 138 4511 4509 48 7 29 32 2 3 1412 1200 1172 0 0
oligos_8nt_mkv6_m1_shift1 (oligos_8nt_mkv6_m1)		0.904	0.844	13.155	0.826	0.943	1.278	0.954	17	15	17	10	17	16	17	15.571	8	; oligos_7nt_mkv5_m1 versus oligos_8nt_mkv6_m1; m=1/17; ncol2=15; w=14; offset=-1; strand=D; shift=1; score=15.5714; -atGGTTGCACAATah-- ; cor=0.904; Ncor=0.844; logoDP=13.155; NIcor=0.826; NsEucl=0.943; SSD=1.278; NSW=0.954; rcor=17; rNcor=15; rlogoDP=17; rNIcor=10; rNsEucl=17; rSSD=16; rNSW=17; rank_mean=15.571; match_rank=8 a 0 916 519 193 371 2 4 54 1 2146 57 2247 2242 18 885 631 0 0 c 0 427 233 24 77 4 0 3 2252 32 2134 18 4 475 510 578 0 0 g 0 477 406 1804 1760 2 8 2128 5 32 14 0 14 49 354 370 0 0 t 0 447 1109 246 59 2259 2255 82 9 57 62 2 7 1725 518 688 0 0
positions_7nt_m2_shift0 (positions_7nt_m2)		0.909	0.748	13.549	0.732	0.940	1.411	0.950	16	47	8	32	21	19	19	23.143	14	; oligos_7nt_mkv5_m1 versus positions_7nt_m2; m=2/17; ncol2=17; w=14; offset=-2; strand=D; shift=0; score=23.1429; rmAGATTGCACAACTyt- ; cor=0.909; Ncor=0.748; logoDP=13.549; NIcor=0.732; NsEucl=0.940; SSD=1.411; NSW=0.950; rcor=16; rNcor=47; rlogoDP=8; rNIcor=32; rNsEucl=21; rSSD=19; rNSW=19; rank_mean=23.143; match_rank=14 a 94 132 260 16 314 0 0 10 2 311 7 331 333 6 35 67 73 0 c 71 85 4 10 5 0 0 0 330 11 318 3 0 296 15 105 76 0 g 95 77 9 277 13 1 2 309 1 1 1 0 0 7 2 77 54 0 t 74 40 61 31 2 333 332 15 1 11 8 0 1 25 282 85 131 0
positions_8nt_m3_shift2 (positions_8nt_m3)		0.845	0.845	12.790	0.857	0.929	1.970	0.930	38	14	28	5	35	34	33	26.714	20	; oligos_7nt_mkv5_m1 versus positions_8nt_m3; m=3/17; ncol2=14; w=14; offset=0; strand=D; shift=2; score=26.7143; --wtATTGCCCAATaw-- ; cor=0.845; Ncor=0.845; logoDP=12.790; NIcor=0.857; NsEucl=0.929; SSD=1.970; NSW=0.930; rcor=38; rNcor=14; rlogoDP=28; rNIcor=5; rNsEucl=35; rSSD=34; rNSW=33; rank_mean=26.714; match_rank=20 a 0 0 331 246 842 1 1 12 2 34 5 1110 1118 50 412 284 0 0 c 0 0 229 210 94 0 1 0 1116 933 1097 4 0 179 259 273 0 0 g 0 0 247 258 141 0 1 1104 0 142 4 3 0 80 183 202 0 0 t 0 0 311 404 41 1117 1115 2 0 9 12 1 0 809 264 359 0 0
positions_7nt_m5_shift0 (positions_7nt_m5)		0.889	0.732	13.542	0.721	0.934	1.691	0.940	20	55	9	34	25	26	25	27.714	21	; oligos_7nt_mkv5_m1 versus positions_7nt_m5; m=4/17; ncol2=17; w=14; offset=-2; strand=D; shift=0; score=27.7143; wmACATTGCACAACTsy- ; cor=0.889; Ncor=0.732; logoDP=13.542; NIcor=0.721; NsEucl=0.934; SSD=1.691; NSW=0.940; rcor=20; rNcor=55; rlogoDP=9; rNIcor=34; rNsEucl=25; rSSD=26; rNSW=25; rank_mean=27.714; match_rank=21 a 73 84 193 16 219 0 0 4 0 221 11 226 224 2 20 52 44 0 c 48 64 6 163 4 0 0 0 227 3 213 1 0 205 12 64 62 0 g 45 44 16 18 0 0 3 206 0 1 1 0 1 4 0 58 48 0 t 62 36 13 31 5 228 225 18 1 3 3 1 3 17 196 54 74 0
oligos_8nt_mkv6_m3_rc_shift2 (oligos_8nt_mkv6_m3_rc)		0.868	0.868	10.149	0.702	0.935	1.662	0.941	27	10	71	40	24	25	24	31.571	27	; oligos_7nt_mkv5_m1 versus oligos_8nt_mkv6_m3_rc; m=5/17; ncol2=14; w=14; offset=0; strand=R; shift=2; score=31.5714; --wtATTGCTCAATaw-- ; cor=0.868; Ncor=0.868; logoDP=10.149; NIcor=0.702; NsEucl=0.935; SSD=1.662; NSW=0.941; rcor=27; rNcor=10; rlogoDP=71; rNIcor=40; rNsEucl=24; rSSD=25; rNSW=24; rank_mean=31.571; match_rank=27 a 0 0 955 726 2742 8 7 108 16 677 97 3295 3306 83 1479 930 0 0 c 0 0 676 534 213 4 4 6 3305 96 3053 20 9 325 682 791 0 0 g 0 0 749 657 291 9 10 3149 10 210 9 5 6 180 505 573 0 0 t 0 0 955 1418 89 3314 3314 72 4 2352 176 15 14 2747 669 1041 0 0
positions_8nt_m4_shift0 (positions_8nt_m4)		0.860	0.708	14.112	0.678	0.925	2.189	0.922	31	66	5	45	38	45	39	38.429	31	; oligos_7nt_mkv5_m1 versus positions_8nt_m4; m=6/17; ncol2=17; w=14; offset=-2; strand=D; shift=0; score=38.4286; raTGGTTGCACAAyAwt- ; cor=0.860; Ncor=0.708; logoDP=14.112; NIcor=0.678; NsEucl=0.925; SSD=2.189; NSW=0.922; rcor=31; rNcor=66; rlogoDP=5; rNIcor=45; rNsEucl=38; rSSD=45; rNSW=39; rank_mean=38.429; match_rank=31 a 176 350 19 19 55 1 1 11 1 634 4 646 645 6 548 174 92 0 c 61 81 8 2 8 0 0 2 643 3 635 1 0 239 29 149 112 0 g 352 112 19 612 578 0 0 628 0 5 1 0 0 12 34 147 50 0 t 58 104 601 14 6 646 646 6 3 5 7 0 2 390 36 177 393 0
oligos_8nt_mkv6_m2_rc_shift2 (oligos_8nt_mkv6_m2_rc)		0.850	0.850	8.970	0.557	0.931	1.891	0.932	36	12	80	75	32	31	30	42.286	35	; oligos_7nt_mkv5_m1 versus oligos_8nt_mkv6_m2_rc; m=7/17; ncol2=14; w=14; offset=0; strand=R; shift=2; score=42.2857; --wtATTTCACAATmw-- ; cor=0.850; Ncor=0.850; logoDP=8.970; NIcor=0.557; NsEucl=0.931; SSD=1.891; NSW=0.932; rcor=36; rNcor=12; rlogoDP=80; rNIcor=75; rNsEucl=32; rSSD=31; rNSW=30; rank_mean=42.286; match_rank=35 a 0 0 1173 770 3364 10 29 427 24 3664 23 3968 3993 167 1554 1082 0 0 c 0 0 786 669 246 7 6 11 3990 36 3924 32 8 569 1034 987 0 0 g 0 0 869 982 333 6 63 359 2 263 14 9 10 238 553 658 0 0 t 0 0 1207 1614 92 4012 3937 3238 19 72 74 26 24 3061 894 1308 0 0
oligos_7nt_mkv5_m5_shift3 (oligos_7nt_mkv5_m5)		0.828	0.710	12.989	0.717	0.914	2.153	0.910	45	65	21	37	73	41	52	47.714	41	; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m5; m=8/17; ncol2=12; w=12; offset=1; strand=D; shift=3; score=47.7143; ---wrTTGCTCAAya--- ; cor=0.828; Ncor=0.710; logoDP=12.989; NIcor=0.717; NsEucl=0.914; SSD=2.153; NSW=0.910; rcor=45; rNcor=65; rlogoDP=21; rNIcor=37; rNsEucl=73; rSSD=41; rNSW=52; rank_mean=47.714; match_rank=41 a 0 0 0 790 1154 0 0 0 0 5 0 2774 2774 284 977 0 0 0 c 0 0 0 474 551 0 1 0 2774 0 2774 0 0 848 665 0 0 0 g 0 0 0 595 751 0 0 2774 0 6 0 0 0 483 459 0 0 0 t 0 0 0 915 318 2774 2773 0 0 2763 0 0 0 1159 673 0 0 0
positions_8nt_m1_shift0 (positions_8nt_m1)		0.823	0.720	11.640	0.700	0.921	2.462	0.912	51	59	46	41	44	58	50	49.857	42	; oligos_7nt_mkv5_m1 versus positions_8nt_m1; m=9/17; ncol2=16; w=14; offset=-2; strand=D; shift=0; score=49.8571; amAGATTGCAAAACww-- ; cor=0.823; Ncor=0.720; logoDP=11.640; NIcor=0.700; NsEucl=0.921; SSD=2.462; NSW=0.912; rcor=51; rNcor=59; rlogoDP=46; rNIcor=41; rNsEucl=44; rSSD=58; rNSW=50; rank_mean=49.857; match_rank=42 a 172 182 482 52 497 2 2 12 3 517 451 522 535 8 215 163 0 0 c 112 161 5 27 15 3 0 2 539 6 70 25 3 479 124 119 0 0 g 134 132 23 439 22 2 2 518 5 15 2 2 7 22 43 128 0 0 t 131 74 39 31 15 542 545 17 2 11 26 0 4 40 167 139 0 0
positions_7nt_m1_shift2 (positions_7nt_m1)		0.808	0.754	11.667	0.737	0.919	2.567	0.908	64	43	44	29	49	65	59	50.429	44	; oligos_7nt_mkv5_m1 versus positions_7nt_m1; m=10/17; ncol2=15; w=14; offset=0; strand=D; shift=2; score=50.4286; --wtATTTCACAATCwy- ; cor=0.808; Ncor=0.754; logoDP=11.667; NIcor=0.737; NsEucl=0.919; SSD=2.567; NSW=0.908; rcor=64; rNcor=43; rlogoDP=44; rNIcor=29; rNsEucl=49; rSSD=65; rNSW=59; rank_mean=50.429; match_rank=44 a 0 0 394 218 1344 6 10 132 6 1281 17 1366 1387 18 237 486 348 0 c 0 0 277 242 17 9 7 9 1392 26 1335 33 4 63 1048 300 369 0 g 0 0 313 341 33 4 46 166 3 48 5 1 6 13 43 155 231 0 t 0 0 419 602 9 1384 1340 1096 2 48 46 3 6 1309 75 462 455 0
oligos_8nt_mkv6_m5_shift3 (oligos_8nt_mkv6_m5)		0.824	0.706	12.926	0.720	0.913	2.185	0.909	50	68	23	35	77	44	56	50.429	45	; oligos_7nt_mkv5_m1 versus oligos_8nt_mkv6_m5; m=11/17; ncol2=12; w=12; offset=1; strand=D; shift=3; score=50.4286; ---waTTGCCCAAya--- ; cor=0.824; Ncor=0.706; logoDP=12.926; NIcor=0.720; NsEucl=0.913; SSD=2.185; NSW=0.909; rcor=50; rNcor=68; rlogoDP=23; rNIcor=35; rNsEucl=77; rSSD=44; rNSW=56; rank_mean=50.429; match_rank=45 a 0 0 0 519 683 0 0 0 0 5 0 1878 1880 230 606 0 0 0 c 0 0 0 405 470 0 0 0 1881 1825 1880 0 1 573 394 0 0 0 g 0 0 0 401 453 0 0 1879 0 50 0 3 0 432 449 0 0 0 t 0 0 0 556 275 1881 1881 2 0 1 1 0 0 646 432 0 0 0
oligos_7nt_mkv5_m3_shift3 (oligos_7nt_mkv5_m3)		0.825	0.708	12.567	0.712	0.913	2.177	0.909	49	67	30	38	76	43	54	51.000	46	; oligos_7nt_mkv5_m1 versus oligos_7nt_mkv5_m3; m=12/17; ncol2=12; w=12; offset=1; strand=D; shift=3; score= 51; ---wrTTACACAAya--- ; cor=0.825; Ncor=0.708; logoDP=12.567; NIcor=0.712; NsEucl=0.913; SSD=2.177; NSW=0.909; rcor=49; rNcor=67; rlogoDP=30; rNIcor=38; rNsEucl=76; rSSD=43; rNSW=54; rank_mean=51.000; match_rank=46 a 0 0 0 701 1073 23 1 2580 0 2542 0 2578 2579 307 920 0 0 0 c 0 0 0 409 457 6 0 0 2580 0 2580 0 1 755 634 0 0 0 g 0 0 0 616 697 30 0 0 0 38 0 2 0 388 415 0 0 0 t 0 0 0 854 353 2521 2579 0 0 0 0 0 0 1130 611 0 0 0
oligos_8nt_mkv6_m4_shift3 (oligos_8nt_mkv6_m4)		0.808	0.750	11.571	0.751	0.916	2.379	0.909	63	45	48	24	66	54	58	51.143	47	; oligos_7nt_mkv5_m1 versus oligos_8nt_mkv6_m4; m=13/17; ncol2=13; w=13; offset=1; strand=D; shift=3; score=51.1429; ---wrTTACACAATah-- ; cor=0.808; Ncor=0.750; logoDP=11.571; NIcor=0.751; NsEucl=0.916; SSD=2.379; NSW=0.909; rcor=63; rNcor=45; rlogoDP=48; rNIcor=24; rNsEucl=66; rSSD=54; rNSW=58; rank_mean=51.143; match_rank=47 a 0 0 0 768 1278 9 3 2545 2 2026 1 2529 2545 143 934 674 0 0 c 0 0 0 372 377 3 0 0 2552 7 2516 4 1 447 595 648 0 0 g 0 0 0 562 670 8 10 10 2 516 0 21 8 179 403 433 0 0 t 0 0 0 862 239 2544 2551 9 8 15 47 10 10 1795 632 809 0 0
positions_7nt_m4_shift0 (positions_7nt_m4)		0.816	0.672	12.996	0.661	0.916	2.751	0.902	58	78	20	50	64	74	67	58.714	57	; oligos_7nt_mkv5_m1 versus positions_7nt_m4; m=14/17; ncol2=17; w=14; offset=-2; strand=D; shift=0; score=58.7143; wyCTCTTGCACAACTbh- ; cor=0.816; Ncor=0.672; logoDP=12.996; NIcor=0.661; NsEucl=0.916; SSD=2.751; NSW=0.902; rcor=58; rNcor=78; rlogoDP=20; rNIcor=50; rNsEucl=64; rSSD=74; rNSW=67; rank_mean=58.714; match_rank=57 a 53 47 13 1 20 0 1 2 0 180 11 195 197 3 6 36 50 0 c 42 60 160 8 160 0 0 0 198 8 185 2 1 178 15 53 54 0 g 45 38 9 0 18 0 1 189 1 3 1 1 0 3 3 54 24 0 t 59 54 17 190 1 199 197 8 0 8 2 1 1 15 175 56 71 0
positions_6nt_m4_shift0 (positions_6nt_m4)		0.819	0.637	13.374	0.614	0.914	2.908	0.896	56	87	15	65	72	85	76	65.143	66	; oligos_7nt_mkv5_m1 versus positions_6nt_m4; m=15/17; ncol2=18; w=14; offset=-2; strand=D; shift=0; score=65.1429; wsATGTTGCACAACAGtr ; cor=0.819; Ncor=0.637; logoDP=13.374; NIcor=0.614; NsEucl=0.914; SSD=2.908; NSW=0.896; rcor=56; rNcor=87; rlogoDP=15; rNIcor=65; rNsEucl=72; rSSD=85; rNSW=76; rank_mean=65.143; match_rank=66 a 39 29 88 5 6 0 1 4 2 115 3 118 117 2 106 5 21 32 c 22 32 16 1 4 0 0 0 114 0 110 0 0 110 2 8 25 29 g 27 31 7 0 106 0 0 110 1 0 1 0 0 3 2 99 25 33 t 30 26 7 112 2 118 117 4 1 3 4 0 1 3 8 6 47 24
positions_8nt_m2_rc_shift2 (positions_8nt_m2_rc)		0.826	0.722	0.381	-0.207	0.921	2.446	0.913	48	57	108	110	43	57	48	67.286	70	; oligos_7nt_mkv5_m1 versus positions_8nt_m2_rc; m=16/17; ncol2=16; w=14; offset=0; strand=R; shift=2; score=67.2857; --htcTTGCACAATCAyw ; cor=0.826; Ncor=0.722; logoDP=0.381; NIcor=-0.207; NsEucl=0.921; SSD=2.446; NSW=0.913; rcor=48; rNcor=57; rlogoDP=108; rNIcor=110; rNsEucl=43; rSSD=57; rNSW=48; rank_mean=67.286; match_rank=70 a 0 0 160 131 141 2 0 25 4 601 17 626 629 13 23 558 156 171 c 0 0 165 107 406 4 0 3 632 7 594 10 1 24 576 24 178 140 g 0 0 147 129 72 0 4 586 1 12 4 1 4 12 20 13 131 144 t 0 0 166 271 19 632 634 24 1 18 23 1 4 589 19 43 173 183
positions_6nt_m1_rc_shift3 (positions_6nt_m1_rc)		0.765	0.622	0.444	-0.187	0.904	3.141	0.879	98	98	106	104	92	98	98	99.143	106	; oligos_7nt_mkv5_m1 versus positions_6nt_m1_rc; m=17/17; ncol2=15; w=13; offset=1; strand=R; shift=3; score=99.1429; ---kaTTTCACAATCTww ; cor=0.765; Ncor=0.622; logoDP=0.444; NIcor=-0.187; NsEucl=0.904; SSD=3.141; NSW=0.879; rcor=98; rNcor=98; rlogoDP=106; rNIcor=104; rNsEucl=92; rSSD=98; rNSW=98; rank_mean=99.143; match_rank=106 a 0 0 0 188 538 7 10 87 4 820 5 866 880 4 132 75 243 237 c 0 0 0 107 114 14 5 6 885 7 850 17 3 16 695 31 215 172 g 0 0 0 239 182 2 31 79 1 40 2 2 5 8 23 19 176 127 t 0 0 0 359 59 870 847 721 3 26 36 8 5 865 43 768 259 357

One-to-n matrix alignment; reference matrix: positions_6nt_m1_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
positions_6nt_m1_shift0 (positions_6nt_m1)																		; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=16; wwAGATTGTGAAAtm- ; Alignment reference a 357 259 768 43 865 5 8 36 26 3 721 847 870 59 359 0 c 127 176 19 23 8 5 2 2 40 1 79 31 2 182 239 0 g 172 215 31 695 16 3 17 850 7 885 6 5 14 114 107 0 t 237 243 75 132 4 880 866 5 820 4 87 10 7 538 188 0
positions_7nt_m3_shift0 (positions_7nt_m3)		0.911	0.854	11.818	0.840	0.947	1.284	0.957	15	11	40	7	15	17	15	17.143	9	; positions_6nt_m1 versus positions_7nt_m3; m=1/3; ncol2=16; w=15; offset=0; strand=D; shift=0; score=17.1429; arAGATTGCGAAATrw ; cor=0.911; Ncor=0.854; logoDP=11.818; NIcor=0.840; NsEucl=0.947; SSD=1.284; NSW=0.957; rcor=15; rNcor=11; rlogoDP=40; rNIcor=7; rNsEucl=15; rSSD=17; rNSW=15; rank_mean=17.143; match_rank=9 a 162 113 401 15 413 0 0 7 36 40 396 423 432 2 126 150 c 77 108 4 27 6 0 0 0 303 14 17 10 0 15 102 90 g 98 128 9 350 11 0 1 422 24 365 2 0 1 7 112 76 t 96 84 19 41 3 433 432 4 70 14 18 0 0 409 93 117
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)		0.958	0.838	4.417	0.161	0.961	0.583	0.979	7	17	89	90	4	5	5	31.000	26	; positions_6nt_m1 versus positions_7nt_m1_rc; m=2/3; ncol2=15; w=14; offset=1; strand=R; shift=1; score= 31; -rwGATTGTGAAATaw ; cor=0.958; Ncor=0.838; logoDP=4.417; NIcor=0.161; NsEucl=0.961; SSD=0.583; NSW=0.979; rcor=7; rNcor=17; rlogoDP=89; rNIcor=90; rNsEucl=4; rSSD=5; rNSW=5; rank_mean=31.000; match_rank=26 a 0 455 462 75 1309 6 3 46 48 2 1096 1340 1384 9 602 419 c 0 231 155 43 13 6 1 5 48 3 166 46 4 33 341 313 g 0 369 300 1048 63 4 33 1335 26 1392 9 7 9 17 242 277 t 0 348 486 237 18 1387 1366 17 1281 6 132 10 6 1344 218 394
positions_8nt_m2_shift0 (positions_8nt_m2)		0.791	0.742	11.797	0.737	0.918	3.019	0.899	77	50	41	28	53	90	69	58.286	56	; positions_6nt_m1 versus positions_8nt_m2; m=3/3; ncol2=16; w=15; offset=0; strand=D; shift=0; score=58.2857; wrTGATTGTGCAAgad ; cor=0.791; Ncor=0.742; logoDP=11.797; NIcor=0.737; NsEucl=0.918; SSD=3.019; NSW=0.899; rcor=77; rNcor=50; rlogoDP=41; rNIcor=28; rNsEucl=53; rSSD=90; rNSW=69; rank_mean=58.286; match_rank=56 a 183 173 43 19 589 4 1 23 18 1 24 634 632 19 271 166 c 144 131 13 20 12 4 1 4 12 1 586 4 0 72 129 147 g 140 178 24 576 24 1 10 594 7 632 3 0 4 406 107 165 t 171 156 558 23 13 629 626 17 601 4 25 0 2 141 131 160

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift2 ; 18 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m1_shift2 (oligos_6nt_mkv4_m1)																		; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=15; shift=2; ncol=17; --dkATTGTGCAATCwt ; Alignment reference a 0 0 1017 719 2822 11 5 121 129 5 243 3289 3292 59 474 1377 760 c 0 0 520 532 95 7 0 18 37 1 2929 18 4 304 2259 685 751 g 0 0 845 848 350 11 35 3067 63 3295 7 1 5 76 297 337 623 t 0 0 927 1210 42 3280 3269 103 3080 8 130 1 8 2870 279 910 1175
oligos_8nt_mkv6_m3_shift2 (oligos_8nt_mkv6_m3)		0.896	0.836	11.651	0.831	0.941	1.364	0.951	19	18	45	9	19	18	18	20.857	11	; oligos_6nt_mkv4_m1 versus oligos_8nt_mkv6_m3; m=1/17; ncol2=14; w=14; offset=0; strand=D; shift=2; score=20.8571; --wtATTGAGCAATaw- ; cor=0.896; Ncor=0.836; logoDP=11.651; NIcor=0.831; NsEucl=0.941; SSD=1.364; NSW=0.951; rcor=19; rNcor=18; rlogoDP=45; rNIcor=9; rNsEucl=19; rSSD=18; rNSW=18; rank_mean=20.857; match_rank=11 a 0 0 1041 669 2747 14 15 176 2352 4 72 3314 3314 89 1418 955 0 c 0 0 573 505 180 6 5 9 210 10 3149 10 9 291 657 749 0 g 0 0 791 682 325 9 20 3053 96 3305 6 4 4 213 534 676 0 t 0 0 930 1479 83 3306 3295 97 677 16 108 7 8 2742 726 955 0
oligos_8nt_mkv6_m2_shift2 (oligos_8nt_mkv6_m2)		0.886	0.827	11.587	0.824	0.938	1.492	0.947	23	22	47	11	23	20	21	23.857	15	; oligos_6nt_mkv4_m1 versus oligos_8nt_mkv6_m2; m=2/17; ncol2=14; w=14; offset=0; strand=D; shift=2; score=23.8571; --wkATTGTGAAATaw- ; cor=0.886; Ncor=0.827; logoDP=11.587; NIcor=0.824; NsEucl=0.938; SSD=1.492; NSW=0.947; rcor=23; rNcor=22; rlogoDP=47; rNIcor=11; rNsEucl=23; rSSD=20; rNSW=21; rank_mean=23.857; match_rank=15 a 0 0 1308 894 3061 24 26 74 72 19 3238 3937 4012 92 1614 1207 0 c 0 0 658 553 238 10 9 14 263 2 359 63 6 333 982 869 0 g 0 0 987 1034 569 8 32 3924 36 3990 11 6 7 246 669 786 0 t 0 0 1082 1554 167 3993 3968 23 3664 24 427 29 10 3364 770 1173 0
oligos_7nt_mkv5_m1_rc_shift2 (oligos_7nt_mkv5_m1_rc)		0.942	0.879	9.973	0.606	0.956	0.768	0.973	9	9	73	67	9	9	9	26.429	17	; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m1_rc; m=3/17; ncol2=14; w=14; offset=0; strand=R; shift=2; score=26.4286; --dwrTTGTGCAATmw- ; cor=0.942; Ncor=0.879; logoDP=9.973; NIcor=0.606; NsEucl=0.956; SSD=0.768; NSW=0.973; rcor=9; rNcor=9; rlogoDP=73; rNIcor=67; rNsEucl=9; rSSD=9; rNSW=9; rank_mean=26.429; match_rank=17 a 0 0 1172 1200 1412 3 2 32 29 7 48 4509 4511 138 1413 1671 0 c 0 0 930 502 337 3 4 5 107 2 4418 3 4 915 1532 861 0 g 0 0 1193 988 2623 3 9 4467 16 4509 3 4 3 307 719 816 0 t 0 0 1226 1831 149 4512 4506 17 4369 3 52 5 3 3161 857 1173 0
oligos_6nt_mkv4_m5_rc_shift2 (oligos_6nt_mkv4_m5_rc)		0.921	0.921	4.127	0.083	0.951	1.080	0.964	14	3	94	94	13	13	14	35.000	28	; oligos_6nt_mkv4_m1 versus oligos_6nt_mkv4_m5_rc; m=4/17; ncol2=15; w=15; offset=0; strand=R; shift=2; score= 35; --rwGTTGTGCAATCat ; cor=0.921; Ncor=0.921; logoDP=4.127; NIcor=0.083; NsEucl=0.951; SSD=1.080; NSW=0.964; rcor=14; rNcor=3; rlogoDP=94; rNIcor=94; rNsEucl=13; rSSD=13; rNSW=14; rank_mean=35.000; match_rank=28 a 0 0 696 784 370 9 1 83 88 9 209 2703 2706 44 252 1329 620 c 0 0 539 166 95 9 1 16 31 2 2428 10 4 474 2160 483 578 g 0 0 803 613 2208 10 26 2522 51 2698 6 1 4 56 158 240 471 t 0 0 677 1152 42 2687 2687 94 2545 6 72 1 1 2141 145 663 1046
oligos_8nt_mkv6_m1_rc_shift2 (oligos_8nt_mkv6_m1_rc)		0.925	0.925	3.998	0.027	0.952	1.023	0.966	13	2	96	99	12	12	12	35.143	29	; oligos_6nt_mkv4_m1 versus oligos_8nt_mkv6_m1_rc; m=5/17; ncol2=15; w=15; offset=0; strand=R; shift=2; score=35.1429; --dtATTGTGCAACCat ; cor=0.925; Ncor=0.925; logoDP=3.998; NIcor=0.027; NsEucl=0.952; SSD=1.023; NSW=0.966; rcor=13; rNcor=2; rlogoDP=96; rNIcor=99; rNsEucl=12; rSSD=12; rNSW=12; rank_mean=35.143; match_rank=29 a 0 0 688 518 1725 7 2 62 57 9 82 2255 2259 59 246 1109 447 c 0 0 370 354 49 14 0 14 32 5 2128 8 2 1760 1804 406 477 g 0 0 578 510 475 4 18 2134 32 2252 3 0 4 77 24 233 427 t 0 0 631 885 18 2242 2247 57 2146 1 54 4 2 371 193 519 916
positions_8nt_m3_rc_shift2 (positions_8nt_m3_rc)		0.858	0.801	10.337	0.675	0.931	1.865	0.933	33	28	67	46	30	30	29	37.571	30	; oligos_6nt_mkv4_m1 versus positions_8nt_m3_rc; m=6/17; ncol2=14; w=14; offset=0; strand=R; shift=2; score=37.5714; --wtATTGGGCAATaw- ; cor=0.858; Ncor=0.801; logoDP=10.337; NIcor=0.675; NsEucl=0.931; SSD=1.865; NSW=0.933; rcor=33; rNcor=28; rlogoDP=67; rNIcor=46; rNsEucl=30; rSSD=30; rNSW=29; rank_mean=37.571; match_rank=30 a 0 0 359 264 809 0 1 12 9 0 2 1115 1117 41 404 311 0 c 0 0 202 183 80 0 3 4 142 0 1104 1 0 141 258 247 0 g 0 0 273 259 179 0 4 1097 933 1116 0 1 0 94 210 229 0 t 0 0 284 412 50 1118 1110 5 34 2 12 1 1 842 246 331 0
positions_8nt_m2_shift0 (positions_8nt_m2)		0.843	0.694	12.271	0.686	0.924	2.244	0.920	40	72	32	42	39	48	40	44.714	38	; oligos_6nt_mkv4_m1 versus positions_8nt_m2; m=7/17; ncol2=16; w=14; offset=-2; strand=D; shift=0; score=44.7143; wrTGATTGTGCAAgad- ; cor=0.843; Ncor=0.694; logoDP=12.271; NIcor=0.686; NsEucl=0.924; SSD=2.244; NSW=0.920; rcor=40; rNcor=72; rlogoDP=32; rNIcor=42; rNsEucl=39; rSSD=48; rNSW=40; rank_mean=44.714; match_rank=38 a 183 173 43 19 589 4 1 23 18 1 24 634 632 19 271 166 0 c 144 131 13 20 12 4 1 4 12 1 586 4 0 72 129 147 0 g 140 178 24 576 24 1 10 594 7 632 3 0 4 406 107 165 0 t 171 156 558 23 13 629 626 17 601 4 25 0 2 141 131 160 0
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)		0.871	0.762	4.226	0.089	0.933	1.762	0.937	26	36	92	93	27	27	26	46.714	40	; oligos_6nt_mkv4_m1 versus positions_7nt_m1_rc; m=8/17; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=46.7143; -rwGATTGTGAAATaw- ; cor=0.871; Ncor=0.762; logoDP=4.226; NIcor=0.089; NsEucl=0.933; SSD=1.762; NSW=0.937; rcor=26; rNcor=36; rlogoDP=92; rNIcor=93; rNsEucl=27; rSSD=27; rNSW=26; rank_mean=46.714; match_rank=40 a 0 455 462 75 1309 6 3 46 48 2 1096 1340 1384 9 602 419 0 c 0 231 155 43 13 6 1 5 48 3 166 46 4 33 341 313 0 g 0 369 300 1048 63 4 33 1335 26 1392 9 7 9 17 242 277 0 t 0 348 486 237 18 1387 1366 17 1281 6 132 10 6 1344 218 394 0
positions_7nt_m2_rc_shift1 (positions_7nt_m2_rc)		0.858	0.757	4.214	0.043	0.931	2.170	0.928	34	40	93	97	31	42	34	53.000	48	; oligos_6nt_mkv4_m1 versus positions_7nt_m2_rc; m=9/17; ncol2=17; w=15; offset=-1; strand=R; shift=1; score= 53; -arAGTTGTGCAATCTk ; cor=0.858; Ncor=0.757; logoDP=4.214; NIcor=0.043; NsEucl=0.931; SSD=2.170; NSW=0.928; rcor=34; rNcor=40; rlogoDP=93; rNIcor=97; rNsEucl=31; rSSD=42; rNSW=34; rank_mean=53.000; match_rank=48 a 0 131 85 282 25 1 0 8 11 1 15 332 333 2 31 61 40 c 0 54 77 2 7 0 0 1 1 1 309 2 1 13 277 9 77 g 0 76 105 15 296 0 3 318 11 330 0 0 0 5 10 4 85 t 0 73 67 35 6 333 331 7 311 2 10 0 0 314 16 260 132
positions_8nt_m4_rc_shift1 (positions_8nt_m4_rc)		0.859	0.758	4.110	0.026	0.930	2.231	0.926	32	38	95	100	34	46	36	54.429	51	; oligos_6nt_mkv4_m1 versus positions_8nt_m4_rc; m=10/17; ncol2=17; w=15; offset=-1; strand=R; shift=1; score=54.4286; -awTrTTGTGCAACCAt ; cor=0.859; Ncor=0.758; logoDP=4.110; NIcor=0.026; NsEucl=0.930; SSD=2.231; NSW=0.926; rcor=32; rNcor=38; rlogoDP=95; rNIcor=100; rNsEucl=34; rSSD=46; rNSW=36; rank_mean=54.429; match_rank=51 a 0 393 177 36 390 2 0 7 5 3 6 646 646 6 14 601 104 c 0 50 147 34 12 0 0 1 5 0 628 0 0 578 612 19 112 g 0 112 149 29 239 0 1 635 3 643 2 0 0 8 2 8 81 t 0 92 174 548 6 645 646 4 634 1 11 1 1 55 19 19 350
positions_6nt_m1_shift0 (positions_6nt_m1)		0.829	0.634	11.241	0.617	0.917	2.335	0.910	43	90	54	64	62	52	53	59.714	58	; oligos_6nt_mkv4_m1 versus positions_6nt_m1; m=11/17; ncol2=15; w=13; offset=-2; strand=D; shift=0; score=59.7143; wwAGATTGTGAAAtm-- ; cor=0.829; Ncor=0.634; logoDP=11.241; NIcor=0.617; NsEucl=0.917; SSD=2.335; NSW=0.910; rcor=43; rNcor=90; rlogoDP=54; rNIcor=64; rNsEucl=62; rSSD=52; rNSW=53; rank_mean=59.714; match_rank=58 a 357 259 768 43 865 5 8 36 26 3 721 847 870 59 359 0 0 c 127 176 19 23 8 5 2 2 40 1 79 31 2 182 239 0 0 g 172 215 31 695 16 3 17 850 7 885 6 5 14 114 107 0 0 t 237 243 75 132 4 880 866 5 820 4 87 10 7 538 188 0 0
oligos_8nt_mkv6_m4_rc_shift2 (oligos_8nt_mkv6_m4_rc)		0.823	0.713	3.759	0.050	0.918	2.273	0.913	52	62	99	96	54	50	49	66.000	68	; oligos_6nt_mkv4_m1 versus oligos_8nt_mkv6_m4_rc; m=12/17; ncol2=13; w=13; offset=0; strand=R; shift=2; score= 66; --dtATTGTGTAAyw-- ; cor=0.823; Ncor=0.713; logoDP=3.759; NIcor=0.050; NsEucl=0.918; SSD=2.273; NSW=0.913; rcor=52; rNcor=62; rlogoDP=99; rNIcor=96; rNsEucl=54; rSSD=50; rNSW=49; rank_mean=66.000; match_rank=68 a 0 0 809 632 1795 10 10 47 15 8 9 2551 2544 239 862 0 0 c 0 0 433 403 179 8 21 0 516 2 10 10 8 670 562 0 0 g 0 0 648 595 447 1 4 2516 7 2552 0 0 3 377 372 0 0 t 0 0 674 934 143 2545 2529 1 2026 2 2545 3 9 1278 768 0 0
positions_8nt_m1_rc_shift2 (positions_8nt_m1_rc)		0.784	0.735	6.910	0.386	0.918	3.063	0.898	84	53	86	85	57	92	72	75.571	81	; oligos_6nt_mkv4_m1 versus positions_8nt_m1_rc; m=13/17; ncol2=16; w=15; offset=0; strand=R; shift=2; score=75.5714; --wwGTTTTGCAATCTk ; cor=0.784; Ncor=0.735; logoDP=6.910; NIcor=0.386; NsEucl=0.918; SSD=3.063; NSW=0.898; rcor=84; rNcor=53; rlogoDP=86; rNIcor=85; rNsEucl=57; rSSD=92; rNSW=72; rank_mean=75.571; match_rank=81 a 0 0 139 167 40 4 0 26 11 2 17 545 542 15 31 39 74 c 0 0 128 43 22 7 2 2 15 5 518 2 2 22 439 23 132 g 0 0 119 124 479 3 25 70 6 539 2 0 3 15 27 5 161 t 0 0 163 215 8 535 522 451 517 3 12 2 2 497 52 482 182
oligos_7nt_mkv5_m3_rc_shift3 (oligos_7nt_mkv5_m3_rc)		0.805	0.644	8.453	0.402	0.907	2.505	0.896	66	85	83	84	88	59	77	77.429	86	; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m3_rc; m=14/17; ncol2=12; w=12; offset=1; strand=R; shift=3; score=77.4286; ---trTTGTGTAAyw-- ; cor=0.805; Ncor=0.644; logoDP=8.453; NIcor=0.402; NsEucl=0.907; SSD=2.505; NSW=0.896; rcor=66; rNcor=85; rlogoDP=83; rNIcor=84; rNsEucl=88; rSSD=59; rNSW=77; rank_mean=77.429; match_rank=86 a 0 0 0 611 1130 0 0 0 0 0 0 2579 2521 353 854 0 0 c 0 0 0 415 388 0 2 0 38 0 0 0 30 697 616 0 0 g 0 0 0 634 755 1 0 2580 0 2580 0 0 6 457 409 0 0 t 0 0 0 920 307 2579 2578 0 2542 0 2580 1 23 1073 701 0 0
oligos_7nt_mkv5_m5_rc_shift3 (oligos_7nt_mkv5_m5_rc)		0.795	0.636	9.963	0.510	0.904	2.644	0.890	74	88	74	78	90	68	82	79.143	88	; oligos_6nt_mkv4_m1 versus oligos_7nt_mkv5_m5_rc; m=15/17; ncol2=12; w=12; offset=1; strand=R; shift=3; score=79.1429; ---trTTGAGCAAyw-- ; cor=0.795; Ncor=0.636; logoDP=9.963; NIcor=0.510; NsEucl=0.904; SSD=2.644; NSW=0.890; rcor=74; rNcor=88; rlogoDP=74; rNIcor=78; rNsEucl=90; rSSD=68; rNSW=82; rank_mean=79.143; match_rank=88 a 0 0 0 673 1159 0 0 0 2763 0 0 2773 2774 318 915 0 0 c 0 0 0 459 483 0 0 0 6 0 2774 0 0 751 595 0 0 g 0 0 0 665 848 0 0 2774 0 2774 0 1 0 551 474 0 0 t 0 0 0 977 284 2774 2774 0 5 0 0 0 0 1154 790 0 0
positions_7nt_m5_rc_shift1 (positions_7nt_m5_rc)		0.796	0.702	4.311	0.041	0.917	3.082	0.897	72	71	90	98	58	95	73	79.571	89	; oligos_6nt_mkv4_m1 versus positions_7nt_m5_rc; m=16/17; ncol2=17; w=15; offset=-1; strand=R; shift=1; score=79.5714; -rsAGTTGTGCAATGTk ; cor=0.796; Ncor=0.702; logoDP=4.311; NIcor=0.041; NsEucl=0.917; SSD=3.082; NSW=0.897; rcor=72; rNcor=71; rlogoDP=90; rNIcor=98; rNsEucl=58; rSSD=95; rNSW=73; rank_mean=79.571; match_rank=89 a 0 74 54 196 17 3 1 3 3 1 18 225 228 5 31 13 36 c 0 48 58 0 4 1 0 1 1 0 206 3 0 0 18 16 44 g 0 62 64 12 205 0 1 213 3 227 0 0 0 4 163 6 64 t 0 44 52 20 2 224 226 11 221 0 4 0 0 219 16 193 84
oligos_8nt_mkv6_m5_rc_shift3 (oligos_8nt_mkv6_m5_rc)		0.781	0.625	9.919	0.500	0.901	2.798	0.883	86	96	75	80	96	77	88	85.429	100	; oligos_6nt_mkv4_m1 versus oligos_8nt_mkv6_m5_rc; m=17/17; ncol2=12; w=12; offset=1; strand=R; shift=3; score=85.4286; ---trTTGGGCAAtw-- ; cor=0.781; Ncor=0.625; logoDP=9.919; NIcor=0.500; NsEucl=0.901; SSD=2.798; NSW=0.883; rcor=86; rNcor=96; rlogoDP=75; rNIcor=80; rNsEucl=96; rSSD=77; rNSW=88; rank_mean=85.429; match_rank=100 a 0 0 0 432 646 0 0 1 1 0 2 1881 1881 275 556 0 0 c 0 0 0 449 432 0 3 0 50 0 1879 0 0 453 401 0 0 g 0 0 0 394 573 1 0 1880 1825 1881 0 0 0 470 405 0 0 t 0 0 0 606 230 1880 1878 0 5 0 0 0 0 683 519 0 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m3_shift2 ; 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
oligos_8nt_mkv6_m3_shift2 (oligos_8nt_mkv6_m3)																		; oligos_8nt_mkv6_m3; m=0 (reference); ncol1=14; shift=2; ncol=16; --wtATTGAGCAATaw ; Alignment reference a 0 0 1041 669 2747 14 15 176 2352 4 72 3314 3314 89 1418 955 c 0 0 573 505 180 6 5 9 210 10 3149 10 9 291 657 749 g 0 0 791 682 325 9 20 3053 96 3305 6 4 4 213 534 676 t 0 0 930 1479 83 3306 3295 97 677 16 108 7 8 2742 726 955
positions_8nt_m3_rc_shift2 (positions_8nt_m3_rc)		0.903	0.903	10.460	0.770	0.944	1.215	0.957	18	7	66	21	16	15	16	22.714	13	; oligos_8nt_mkv6_m3 versus positions_8nt_m3_rc; m=1/6; ncol2=14; w=14; offset=0; strand=R; shift=2; score=22.7143; --wtATTGGGCAATaw ; cor=0.903; Ncor=0.903; logoDP=10.460; NIcor=0.770; NsEucl=0.944; SSD=1.215; NSW=0.957; rcor=18; rNcor=7; rlogoDP=66; rNIcor=21; rNsEucl=16; rSSD=15; rNSW=16; rank_mean=22.714; match_rank=13 a 0 0 359 264 809 0 1 12 9 0 2 1115 1117 41 404 311 c 0 0 202 183 80 0 3 4 142 0 1104 1 0 141 258 247 g 0 0 273 259 179 0 4 1097 933 1116 0 1 0 94 210 229 t 0 0 284 412 50 1118 1110 5 34 2 12 1 1 842 246 331
oligos_8nt_mkv6_m5_rc_shift3 (oligos_8nt_mkv6_m5_rc)		0.829	0.710	10.180	0.579	0.915	2.084	0.913	44	63	70	74	70	40	47	58.286	55	; oligos_8nt_mkv6_m3 versus oligos_8nt_mkv6_m5_rc; m=2/6; ncol2=12; w=12; offset=1; strand=R; shift=3; score=58.2857; ---trTTGGGCAAtw- ; cor=0.829; Ncor=0.710; logoDP=10.180; NIcor=0.579; NsEucl=0.915; SSD=2.084; NSW=0.913; rcor=44; rNcor=63; rlogoDP=70; rNIcor=74; rNsEucl=70; rSSD=40; rNSW=47; rank_mean=58.286; match_rank=55 a 0 0 0 432 646 0 0 1 1 0 2 1881 1881 275 556 0 c 0 0 0 449 432 0 3 0 50 0 1879 0 0 453 401 0 g 0 0 0 394 573 1 0 1880 1825 1881 0 0 0 470 405 0 t 0 0 0 606 230 1880 1878 0 5 0 0 0 0 683 519 0
positions_8nt_m2_shift0 (positions_8nt_m2)		0.791	0.692	11.352	0.675	0.914	2.893	0.897	78	73	50	47	71	83	74	68.000	71	; oligos_8nt_mkv6_m3 versus positions_8nt_m2; m=3/6; ncol2=16; w=14; offset=-2; strand=D; shift=0; score= 68; wrTGATTGTGCAAgad ; cor=0.791; Ncor=0.692; logoDP=11.352; NIcor=0.675; NsEucl=0.914; SSD=2.893; NSW=0.897; rcor=78; rNcor=73; rlogoDP=50; rNIcor=47; rNsEucl=71; rSSD=83; rNSW=74; rank_mean=68.000; match_rank=71 a 183 173 43 19 589 4 1 23 18 1 24 634 632 19 271 166 c 144 131 13 20 12 4 1 4 12 1 586 4 0 72 129 147 g 140 178 24 576 24 1 10 594 7 632 3 0 4 406 107 165 t 171 156 558 23 13 629 626 17 601 4 25 0 2 141 131 160
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)		0.796	0.743	4.448	0.192	0.917	2.687	0.904	73	49	88	88	59	70	63	70.000	74	; oligos_8nt_mkv6_m3 versus positions_7nt_m1_rc; m=4/6; ncol2=15; w=14; offset=-1; strand=R; shift=1; score= 70; -rwGATTGTGAAATaw ; cor=0.796; Ncor=0.743; logoDP=4.448; NIcor=0.192; NsEucl=0.917; SSD=2.687; NSW=0.904; rcor=73; rNcor=49; rlogoDP=88; rNIcor=88; rNsEucl=59; rSSD=70; rNSW=63; rank_mean=70.000; match_rank=74 a 0 455 462 75 1309 6 3 46 48 2 1096 1340 1384 9 602 419 c 0 231 155 43 13 6 1 5 48 3 166 46 4 33 341 313 g 0 369 300 1048 63 4 33 1335 26 1392 9 7 9 17 242 277 t 0 348 486 237 18 1387 1366 17 1281 6 132 10 6 1344 218 394
oligos_8nt_mkv6_m4_rc_shift2 (oligos_8nt_mkv6_m4_rc)		0.765	0.710	3.927	0.128	0.908	2.861	0.890	99	64	97	92	83	81	81	85.286	99	; oligos_8nt_mkv6_m3 versus oligos_8nt_mkv6_m4_rc; m=5/6; ncol2=13; w=13; offset=0; strand=R; shift=2; score=85.2857; --dtATTGTGTAAyw- ; cor=0.765; Ncor=0.710; logoDP=3.927; NIcor=0.128; NsEucl=0.908; SSD=2.861; NSW=0.890; rcor=99; rNcor=64; rlogoDP=97; rNIcor=92; rNsEucl=83; rSSD=81; rNSW=81; rank_mean=85.286; match_rank=99 a 0 0 809 632 1795 10 10 47 15 8 9 2551 2544 239 862 0 c 0 0 433 403 179 8 21 0 516 2 10 10 8 670 562 0 g 0 0 648 595 447 1 4 2516 7 2552 0 0 3 377 372 0 t 0 0 674 934 143 2545 2529 1 2026 2 2545 3 9 1278 768 0
positions_6nt_m1_shift0 (positions_6nt_m1)		0.751	0.610	10.131	0.590	0.901	3.292	0.873	111	103	72	71	97	101	105	94.286	105	; oligos_8nt_mkv6_m3 versus positions_6nt_m1; m=6/6; ncol2=15; w=13; offset=-2; strand=D; shift=0; score=94.2857; wwAGATTGTGAAAtm- ; cor=0.751; Ncor=0.610; logoDP=10.131; NIcor=0.590; NsEucl=0.901; SSD=3.292; NSW=0.873; rcor=111; rNcor=103; rlogoDP=72; rNIcor=71; rNsEucl=97; rSSD=101; rNSW=105; rank_mean=94.286; match_rank=105 a 357 259 768 43 865 5 8 36 26 3 721 847 870 59 359 0 c 127 176 19 23 8 5 2 2 40 1 79 31 2 182 239 0 g 172 215 31 695 16 3 17 850 7 885 6 5 14 114 107 0 t 237 243 75 132 4 880 866 5 820 4 87 10 7 538 188 0

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m2_shift2 ; 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_8nt_mkv6_m2_shift2 (oligos_8nt_mkv6_m2)																		; oligos_8nt_mkv6_m2; m=0 (reference); ncol1=14; shift=2; ncol=16; --wkATTGTGAAATaw ; Alignment reference a 0 0 1308 894 3061 24 26 74 72 19 3238 3937 4012 92 1614 1207 c 0 0 658 553 238 10 9 14 263 2 359 63 6 333 982 869 g 0 0 987 1034 569 8 32 3924 36 3990 11 6 7 246 669 786 t 0 0 1082 1554 167 3993 3968 23 3664 24 427 29 10 3364 770 1173
positions_6nt_m1_shift0 (positions_6nt_m1)		0.933	0.758	11.077	0.744	0.948	0.901	0.965	11	39	59	25	14	10	13	24.429	16	; oligos_8nt_mkv6_m2 versus positions_6nt_m1; m=1/7; ncol2=15; w=13; offset=-2; strand=D; shift=0; score=24.4286; wwAGATTGTGAAAtm- ; cor=0.933; Ncor=0.758; logoDP=11.077; NIcor=0.744; NsEucl=0.948; SSD=0.901; NSW=0.965; rcor=11; rNcor=39; rlogoDP=59; rNIcor=25; rNsEucl=14; rSSD=10; rNSW=13; rank_mean=24.429; match_rank=16 a 357 259 768 43 865 5 8 36 26 3 721 847 870 59 359 0 c 127 176 19 23 8 5 2 2 40 1 79 31 2 182 239 0 g 172 215 31 695 16 3 17 850 7 885 6 5 14 114 107 0 t 237 243 75 132 4 880 866 5 820 4 87 10 7 538 188 0
positions_7nt_m1_rc_shift1 (positions_7nt_m1_rc)		0.970	0.905	4.640	0.213	0.968	0.409	0.985	2	5	87	87	2	2	2	26.714	19	; oligos_8nt_mkv6_m2 versus positions_7nt_m1_rc; m=2/7; ncol2=15; w=14; offset=-1; strand=R; shift=1; score=26.7143; -rwGATTGTGAAATaw ; cor=0.970; Ncor=0.905; logoDP=4.640; NIcor=0.213; NsEucl=0.968; SSD=0.409; NSW=0.985; rcor=2; rNcor=5; rlogoDP=87; rNIcor=87; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=26.714; match_rank=19 a 0 455 462 75 1309 6 3 46 48 2 1096 1340 1384 9 602 419 c 0 231 155 43 13 6 1 5 48 3 166 46 4 33 341 313 g 0 369 300 1048 63 4 33 1335 26 1392 9 7 9 17 242 277 t 0 348 486 237 18 1387 1366 17 1281 6 132 10 6 1344 218 394
positions_7nt_m3_shift0 (positions_7nt_m3)		0.853	0.746	11.101	0.724	0.928	2.029	0.928	35	48	58	33	36	36	35	40.143	33	; oligos_8nt_mkv6_m2 versus positions_7nt_m3; m=3/7; ncol2=16; w=14; offset=-2; strand=D; shift=0; score=40.1429; arAGATTGCGAAATrw ; cor=0.853; Ncor=0.746; logoDP=11.101; NIcor=0.724; NsEucl=0.928; SSD=2.029; NSW=0.928; rcor=35; rNcor=48; rlogoDP=58; rNIcor=33; rNsEucl=36; rSSD=36; rNSW=35; rank_mean=40.143; match_rank=33 a 162 113 401 15 413 0 0 7 36 40 396 423 432 2 126 150 c 77 108 4 27 6 0 0 0 303 14 17 10 0 15 102 90 g 98 128 9 350 11 0 1 422 24 365 2 0 1 7 112 76 t 96 84 19 41 3 433 432 4 70 14 18 0 0 409 93 117
oligos_8nt_mkv6_m3_shift2 (oligos_8nt_mkv6_m3)		0.811	0.811	10.500	0.808	0.923	2.340	0.916	61	25	64	15	41	53	43	43.143	37	; oligos_8nt_mkv6_m2 versus oligos_8nt_mkv6_m3; m=4/7; ncol2=14; w=14; offset=0; strand=D; shift=2; score=43.1429; --wtATTGAGCAATaw ; cor=0.811; Ncor=0.811; logoDP=10.500; NIcor=0.808; NsEucl=0.923; SSD=2.340; NSW=0.916; rcor=61; rNcor=25; rlogoDP=64; rNIcor=15; rNsEucl=41; rSSD=53; rNSW=43; rank_mean=43.143; match_rank=37 a 0 0 1041 669 2747 14 15 176 2352 4 72 3314 3314 89 1418 955 c 0 0 573 505 180 6 5 9 210 10 3149 10 9 291 657 749 g 0 0 791 682 325 9 20 3053 96 3305 6 4 4 213 534 676 t 0 0 930 1479 83 3306 3295 97 677 16 108 7 8 2742 726 955
oligos_8nt_mkv6_m4_rc_shift2 (oligos_8nt_mkv6_m4_rc)		0.865	0.803	4.266	0.168	0.930	1.646	0.937	28	27	91	89	33	24	27	45.571	39	; oligos_8nt_mkv6_m2 versus oligos_8nt_mkv6_m4_rc; m=5/7; ncol2=13; w=13; offset=0; strand=R; shift=2; score=45.5714; --dtATTGTGTAAyw- ; cor=0.865; Ncor=0.803; logoDP=4.266; NIcor=0.168; NsEucl=0.930; SSD=1.646; NSW=0.937; rcor=28; rNcor=27; rlogoDP=91; rNIcor=89; rNsEucl=33; rSSD=24; rNSW=27; rank_mean=45.571; match_rank=39 a 0 0 809 632 1795 10 10 47 15 8 9 2551 2544 239 862 0 c 0 0 433 403 179 8 21 0 516 2 10 10 8 670 562 0 g 0 0 648 595 447 1 4 2516 7 2552 0 0 3 377 372 0 t 0 0 674 934 143 2545 2529 1 2026 2 2545 3 9 1278 768 0
positions_8nt_m3_rc_shift2 (positions_8nt_m3_rc)		0.766	0.766	9.334	0.629	0.914	2.931	0.895	95	35	78	55	74	88	78	71.857	76	; oligos_8nt_mkv6_m2 versus positions_8nt_m3_rc; m=6/7; ncol2=14; w=14; offset=0; strand=R; shift=2; score=71.8571; --wtATTGGGCAATaw ; cor=0.766; Ncor=0.766; logoDP=9.334; NIcor=0.629; NsEucl=0.914; SSD=2.931; NSW=0.895; rcor=95; rNcor=35; rlogoDP=78; rNIcor=55; rNsEucl=74; rSSD=88; rNSW=78; rank_mean=71.857; match_rank=76 a 0 0 359 264 809 0 1 12 9 0 2 1115 1117 41 404 311 c 0 0 202 183 80 0 3 4 142 0 1104 1 0 141 258 247 g 0 0 273 259 179 0 4 1097 933 1116 0 1 0 94 210 229 t 0 0 284 412 50 1118 1110 5 34 2 12 1 1 842 246 331
positions_8nt_m2_shift0 (positions_8nt_m2)		0.774	0.677	11.146	0.663	0.911	3.126	0.888	88	76	56	49	79	97	84	75.571	82	; oligos_8nt_mkv6_m2 versus positions_8nt_m2; m=7/7; ncol2=16; w=14; offset=-2; strand=D; shift=0; score=75.5714; wrTGATTGTGCAAgad ; cor=0.774; Ncor=0.677; logoDP=11.146; NIcor=0.663; NsEucl=0.911; SSD=3.126; NSW=0.888; rcor=88; rNcor=76; rlogoDP=56; rNIcor=49; rNsEucl=79; rSSD=97; rNSW=84; rank_mean=75.571; match_rank=82 a 183 173 43 19 589 4 1 23 18 1 24 634 632 19 271 166 c 144 131 13 20 12 4 1 4 12 1 586 4 0 72 129 147 g 140 178 24 576 24 1 10 594 7 632 3 0 4 406 107 165 t 171 156 558 23 13 629 626 17 601 4 25 0 2 141 131 160

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift2 ; 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_7nt_mkv5_m5_shift2 (oligos_7nt_mkv5_m5)																		; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=12; shift=2; ncol=16; --wrTTGCTCAAya-- ; Alignment reference a 0 0 790 1154 0 0 0 0 5 0 2774 2774 284 977 0 0 c 0 0 474 551 0 1 0 2774 0 2774 0 0 848 665 0 0 g 0 0 595 751 0 0 2774 0 6 0 0 0 483 459 0 0 t 0 0 915 318 2774 2773 0 0 2763 0 0 0 1159 673 0 0
oligos_8nt_mkv6_m3_rc_shift1 (oligos_8nt_mkv6_m3_rc)		0.949	0.814	10.217	0.590	0.953	0.624	0.974	8	24	68	72	11	6	8	28.143	22	; oligos_7nt_mkv5_m5 versus oligos_8nt_mkv6_m3_rc; m=1/5; ncol2=14; w=12; offset=-1; strand=R; shift=1; score=28.1429; -wtATTGCTCAATaw- ; cor=0.949; Ncor=0.814; logoDP=10.217; NIcor=0.590; NsEucl=0.953; SSD=0.624; NSW=0.974; rcor=8; rNcor=24; rlogoDP=68; rNIcor=72; rNsEucl=11; rSSD=6; rNSW=8; rank_mean=28.143; match_rank=22 a 0 955 726 2742 8 7 108 16 677 97 3295 3306 83 1479 930 0 c 0 676 534 213 4 4 6 3305 96 3053 20 9 325 682 791 0 g 0 749 657 291 9 10 3149 10 210 9 5 6 180 505 573 0 t 0 955 1418 89 3314 3314 72 4 2352 176 15 14 2747 669 1041 0
oligos_8nt_mkv6_m5_shift2 (oligos_8nt_mkv6_m5)		0.838	0.838	13.405	0.856	0.918	1.960	0.918	42	16	14	6	56	33	41	29.714	25	; oligos_7nt_mkv5_m5 versus oligos_8nt_mkv6_m5; m=2/5; ncol2=12; w=12; offset=0; strand=D; shift=2; score=29.7143; --waTTGCCCAAya-- ; cor=0.838; Ncor=0.838; logoDP=13.405; NIcor=0.856; NsEucl=0.918; SSD=1.960; NSW=0.918; rcor=42; rNcor=16; rlogoDP=14; rNIcor=6; rNsEucl=56; rSSD=33; rNSW=41; rank_mean=29.714; match_rank=25 a 0 0 519 683 0 0 0 0 5 0 1878 1880 230 606 0 0 c 0 0 405 470 0 0 0 1881 1825 1880 0 1 573 394 0 0 g 0 0 401 453 0 0 1879 0 50 0 3 0 432 449 0 0 t 0 0 556 275 1881 1881 2 0 1 1 0 0 646 432 0 0
positions_8nt_m3_shift1 (positions_8nt_m3)		0.841	0.721	13.041	0.733	0.917	1.978	0.918	41	58	18	31	60	35	42	40.714	34	; oligos_7nt_mkv5_m5 versus positions_8nt_m3; m=3/5; ncol2=14; w=12; offset=-1; strand=D; shift=1; score=40.7143; -wtATTGCCCAATaw- ; cor=0.841; Ncor=0.721; logoDP=13.041; NIcor=0.733; NsEucl=0.917; SSD=1.978; NSW=0.918; rcor=41; rNcor=58; rlogoDP=18; rNIcor=31; rNsEucl=60; rSSD=35; rNSW=42; rank_mean=40.714; match_rank=34 a 0 331 246 842 1 1 12 2 34 5 1110 1118 50 412 284 0 c 0 229 210 94 0 1 0 1116 933 1097 4 0 179 259 273 0 g 0 247 258 141 0 1 1104 0 142 4 3 0 80 183 202 0 t 0 311 404 41 1117 1115 2 0 9 12 1 0 809 264 359 0
oligos_8nt_mkv6_m1_shift0 (oligos_8nt_mkv6_m1)		0.783	0.626	12.202	0.620	0.901	2.814	0.883	85	95	33	62	98	79	89	77.286	85	; oligos_7nt_mkv5_m5 versus oligos_8nt_mkv6_m1; m=4/5; ncol2=15; w=12; offset=-2; strand=D; shift=0; score=77.2857; atGGTTGCACAATah- ; cor=0.783; Ncor=0.626; logoDP=12.202; NIcor=0.620; NsEucl=0.901; SSD=2.814; NSW=0.883; rcor=85; rNcor=95; rlogoDP=33; rNIcor=62; rNsEucl=98; rSSD=79; rNSW=89; rank_mean=77.286; match_rank=85 a 916 519 193 371 2 4 54 1 2146 57 2247 2242 18 885 631 0 c 427 233 24 77 4 0 3 2252 32 2134 18 4 475 510 578 0 g 477 406 1804 1760 2 8 2128 5 32 14 0 14 49 354 370 0 t 447 1109 246 59 2259 2255 82 9 57 62 2 7 1725 518 688 0
positions_8nt_m2_rc_shift1 (positions_8nt_m2_rc)		0.766	0.574	0.256	-0.195	0.897	3.077	0.872	97	106	110	106	106	94	107	103.714	109	; oligos_7nt_mkv5_m5 versus positions_8nt_m2_rc; m=5/5; ncol2=16; w=12; offset=-1; strand=R; shift=1; score=103.714; -htcTTGCACAATCAy ; cor=0.766; Ncor=0.574; logoDP=0.256; NIcor=-0.195; NsEucl=0.897; SSD=3.077; NSW=0.872; rcor=97; rNcor=106; rlogoDP=110; rNIcor=106; rNsEucl=106; rSSD=94; rNSW=107; rank_mean=103.714; match_rank=109 a 0 160 131 141 2 0 25 4 601 17 626 629 13 23 558 156 c 0 165 107 406 4 0 3 632 7 594 10 1 24 576 24 178 g 0 147 129 72 0 4 586 1 12 4 1 4 12 20 13 131 t 0 166 271 19 632 634 24 1 18 23 1 4 589 19 43 173

One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m5_shift0 (positions_7nt_m5)																		; positions_7nt_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; wmACATTGCACAACTsy ; Alignment reference a 73 84 193 16 219 0 0 4 0 221 11 226 224 2 20 52 44 c 48 64 6 163 4 0 0 0 227 3 213 1 0 205 12 64 62 g 45 44 16 18 0 0 3 206 0 1 1 0 1 4 0 58 48 t 62 36 13 31 5 228 225 18 1 3 3 1 3 17 196 54 74
positions_8nt_m1_shift0 (positions_8nt_m1)		0.827	0.778	12.873	0.772	0.927	2.691	0.916	47	31	25	20	37	71	44	39.286	32	; positions_7nt_m5 versus positions_8nt_m1; m=1/1; ncol2=16; w=16; offset=0; strand=D; shift=0; score=39.2857; amAGATTGCAAAACww- ; cor=0.827; Ncor=0.778; logoDP=12.873; NIcor=0.772; NsEucl=0.927; SSD=2.691; NSW=0.916; rcor=47; rNcor=31; rlogoDP=25; rNIcor=20; rNsEucl=37; rSSD=71; rNSW=44; rank_mean=39.286; match_rank=32 a 172 182 482 52 497 2 2 12 3 517 451 522 535 8 215 163 0 c 112 161 5 27 15 3 0 2 539 6 70 25 3 479 124 119 0 g 134 132 23 439 22 2 2 518 5 15 2 2 7 22 43 128 0 t 131 74 39 31 15 542 545 17 2 11 26 0 4 40 167 139 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)																		; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=16; wtATTTCACAATCwy- ; Alignment reference a 394 218 1344 6 10 132 6 1281 17 1366 1387 18 237 486 348 0 c 277 242 17 9 7 9 1392 26 1335 33 4 63 1048 300 369 0 g 313 341 33 4 46 166 3 48 5 1 6 13 43 155 231 0 t 419 602 9 1384 1340 1096 2 48 46 3 6 1309 75 462 455 0
positions_7nt_m3_rc_shift0 (positions_7nt_m3_rc)		0.886	0.831	3.868	0.139	0.940	1.629	0.946	22	20	98	91	22	23	22	42.571	36	; positions_7nt_m1 versus positions_7nt_m3_rc; m=1/2; ncol2=16; w=15; offset=0; strand=R; shift=0; score=42.5714; wyATTTCGCAATCTyt ; cor=0.886; Ncor=0.831; logoDP=3.868; NIcor=0.139; NsEucl=0.940; SSD=1.629; NSW=0.946; rcor=22; rNcor=20; rlogoDP=98; rNIcor=91; rNsEucl=22; rSSD=23; rNSW=22; rank_mean=42.571; match_rank=36 a 117 93 409 0 0 18 14 70 4 432 433 3 41 19 84 96 c 76 112 7 1 0 2 365 24 422 1 0 11 350 9 128 98 g 90 102 15 0 10 17 14 303 0 0 0 6 27 4 108 77 t 150 126 2 432 423 396 40 36 7 0 0 413 15 401 113 162
positions_8nt_m2_rc_shift0 (positions_8nt_m2_rc)		0.820	0.769	1.198	-0.156	0.924	2.586	0.914	55	33	103	103	40	66	45	63.571	64	; positions_7nt_m1 versus positions_8nt_m2_rc; m=2/2; ncol2=16; w=15; offset=0; strand=R; shift=0; score=63.5714; htcTTGCACAATCAyw ; cor=0.820; Ncor=0.769; logoDP=1.198; NIcor=-0.156; NsEucl=0.924; SSD=2.586; NSW=0.914; rcor=55; rNcor=33; rlogoDP=103; rNIcor=103; rNsEucl=40; rSSD=66; rNSW=45; rank_mean=63.571; match_rank=64 a 160 131 141 2 0 25 4 601 17 626 629 13 23 558 156 171 c 165 107 406 4 0 3 632 7 594 10 1 24 576 24 178 140 g 147 129 72 0 4 586 1 12 4 1 4 12 20 13 131 144 t 166 271 19 632 634 24 1 18 23 1 4 589 19 43 173 183

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv6_m4_shift1 ; 5 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_8nt_mkv6_m4_shift1 (oligos_8nt_mkv6_m4)																		; oligos_8nt_mkv6_m4; m=0 (reference); ncol1=13; shift=1; ncol=16; -wrTTACACAATah-- ; Alignment reference a 0 768 1278 9 3 2545 2 2026 1 2529 2545 143 934 674 0 0 c 0 372 377 3 0 0 2552 7 2516 4 1 447 595 648 0 0 g 0 562 670 8 10 10 2 516 0 21 8 179 403 433 0 0 t 0 862 239 2544 2551 9 8 15 47 10 10 1795 632 809 0 0
positions_7nt_m1_shift0 (positions_7nt_m1)		0.828	0.717	10.812	0.703	0.919	2.243	0.914	46	61	62	39	52	47	46	50.429	43	; oligos_8nt_mkv6_m4 versus positions_7nt_m1; m=1/4; ncol2=15; w=13; offset=-1; strand=D; shift=0; score=50.4286; wtATTTCACAATCwy- ; cor=0.828; Ncor=0.717; logoDP=10.812; NIcor=0.703; NsEucl=0.919; SSD=2.243; NSW=0.914; rcor=46; rNcor=61; rlogoDP=62; rNIcor=39; rNsEucl=52; rSSD=47; rNSW=46; rank_mean=50.429; match_rank=43 a 394 218 1344 6 10 132 6 1281 17 1366 1387 18 237 486 348 0 c 277 242 17 9 7 9 1392 26 1335 33 4 63 1048 300 369 0 g 313 341 33 4 46 166 3 48 5 1 6 13 43 155 231 0 t 419 602 9 1384 1340 1096 2 48 46 3 6 1309 75 462 455 0
positions_6nt_m2_shift0 (positions_6nt_m2)		0.798	0.691	10.494	0.663	0.913	2.550	0.902	70	74	65	48	75	62	66	65.714	67	; oligos_8nt_mkv6_m4 versus positions_6nt_m2; m=2/4; ncol2=15; w=13; offset=-1; strand=D; shift=0; score=65.7143; dkATTACGCAAGArw- ; cor=0.798; Ncor=0.691; logoDP=10.494; NIcor=0.663; NsEucl=0.913; SSD=2.550; NSW=0.902; rcor=70; rNcor=74; rlogoDP=65; rNIcor=48; rNsEucl=75; rSSD=62; rNSW=66; rank_mean=65.714; match_rank=67 a 201 156 603 2 1 580 30 65 11 668 668 9 620 178 200 0 c 107 113 23 2 2 3 534 20 638 1 0 57 15 145 138 0 g 172 198 33 1 11 48 28 569 1 0 1 531 14 185 143 0 t 189 202 10 664 655 38 77 15 19 0 0 72 20 161 188 0
positions_6nt_m1_rc_shift1 (positions_6nt_m1_rc)		0.814	0.705	1.962	-0.076	0.915	2.435	0.906	60	69	102	102	68	56	61	74.000	79	; oligos_8nt_mkv6_m4 versus positions_6nt_m1_rc; m=3/4; ncol2=15; w=13; offset=0; strand=R; shift=1; score= 74; -kaTTTCACAATCTww ; cor=0.814; Ncor=0.705; logoDP=1.962; NIcor=-0.076; NsEucl=0.915; SSD=2.435; NSW=0.906; rcor=60; rNcor=69; rlogoDP=102; rNIcor=102; rNsEucl=68; rSSD=56; rNSW=61; rank_mean=74.000; match_rank=79 a 0 188 538 7 10 87 4 820 5 866 880 4 132 75 243 237 c 0 107 114 14 5 6 885 7 850 17 3 16 695 31 215 172 g 0 239 182 2 31 79 1 40 2 2 5 8 23 19 176 127 t 0 359 59 870 847 721 3 26 36 8 5 865 43 768 259 357
positions_8nt_m2_rc_shift0 (positions_8nt_m2_rc)		0.754	0.612	0.498	-0.210	0.900	3.364	0.871	109	102	105	111	100	105	108	105.714	110	; oligos_8nt_mkv6_m4 versus positions_8nt_m2_rc; m=4/4; ncol2=16; w=13; offset=-1; strand=R; shift=0; score=105.714; htcTTGCACAATCAyw ; cor=0.754; Ncor=0.612; logoDP=0.498; NIcor=-0.210; NsEucl=0.900; SSD=3.364; NSW=0.871; rcor=109; rNcor=102; rlogoDP=105; rNIcor=111; rNsEucl=100; rSSD=105; rNSW=108; rank_mean=105.714; match_rank=110 a 160 131 141 2 0 25 4 601 17 626 629 13 23 558 156 171 c 165 107 406 4 0 3 632 7 594 10 1 24 576 24 178 140 g 147 129 72 0 4 586 1 12 4 1 4 12 20 13 131 144 t 166 271 19 632 634 24 1 18 23 1 4 589 19 43 173 183

One-to-n matrix alignment; reference matrix: positions_7nt_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
positions_7nt_m3_shift0 (positions_7nt_m3)																		; positions_7nt_m3; m=0 (reference); ncol1=16; shift=0; ncol=16; arAGATTGCGAAATrw ; Alignment reference a 162 113 401 15 413 0 0 7 36 40 396 423 432 2 126 150 c 77 108 4 27 6 0 0 0 303 14 17 10 0 15 102 90 g 98 128 9 350 11 0 1 422 24 365 2 0 1 7 112 76 t 96 84 19 41 3 433 432 4 70 14 18 0 0 409 93 117
positions_8nt_m1_shift0 (positions_8nt_m1)		0.791	0.791	11.235	0.780	0.923	3.070	0.904	76	30	55	18	42	93	62	53.714	49	; positions_7nt_m3 versus positions_8nt_m1; m=1/1; ncol2=16; w=16; offset=0; strand=D; shift=0; score=53.7143; amAGATTGCAAAACww ; cor=0.791; Ncor=0.791; logoDP=11.235; NIcor=0.780; NsEucl=0.923; SSD=3.070; NSW=0.904; rcor=76; rNcor=30; rlogoDP=55; rNIcor=18; rNsEucl=42; rSSD=93; rNSW=62; rank_mean=53.714; match_rank=49 a 172 182 482 52 497 2 2 12 3 517 451 522 535 8 215 163 c 112 161 5 27 15 3 0 2 539 6 70 25 3 479 124 119 g 134 132 23 439 22 2 2 518 5 15 2 2 7 22 43 128 t 131 74 39 31 15 542 545 17 2 11 26 0 4 40 167 139

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

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m4_shift0 (positions_7nt_m4)																		; positions_7nt_m4; m=0 (reference); ncol1=17; shift=0; ncol=17; wyCTCTTGCACAACTbh ; Alignment reference a 53 47 13 1 20 0 1 2 0 180 11 195 197 3 6 36 50 c 42 60 160 8 160 0 0 0 198 8 185 2 1 178 15 53 54 g 45 38 9 0 18 0 1 189 1 3 1 1 0 3 3 54 24 t 59 54 17 190 1 199 197 8 0 8 2 1 1 15 175 56 71
positions_7nt_m5_shift0 (positions_7nt_m5)		0.767	0.767	13.464	0.767	0.919	3.786	0.889	94	34	10	22	50	107	83	57.143	52	; positions_7nt_m4 versus positions_7nt_m5; m=1/1; ncol2=17; w=17; offset=0; strand=D; shift=0; score=57.1429; wmACATTGCACAACTsy ; cor=0.767; Ncor=0.767; logoDP=13.464; NIcor=0.767; NsEucl=0.919; SSD=3.786; NSW=0.889; rcor=94; rNcor=34; rlogoDP=10; rNIcor=22; rNsEucl=50; rSSD=107; rNSW=83; rank_mean=57.143; match_rank=52 a 73 84 193 16 219 0 0 4 0 221 11 226 224 2 20 52 44 c 48 64 6 163 4 0 0 0 227 3 213 1 0 205 12 64 62 g 45 44 16 18 0 0 3 206 0 1 1 0 1 4 0 58 48 t 62 36 13 31 5 228 225 18 1 3 3 1 3 17 196 54 74

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift6 ; 2 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m2_shift6 (oligos_6nt_mkv4_m2)																		; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=6; ncol=16; ------waCAAAACww ; Alignment reference a 0 0 0 0 0 0 3660 3670 0 9696 9696 9696 9696 0 4475 3410 c 0 0 0 0 0 0 1400 1795 9696 0 0 0 0 9696 1982 2007 g 0 0 0 0 0 0 1654 1877 0 0 0 0 0 0 512 1854 t 0 0 0 0 0 0 2982 2354 0 0 0 0 0 0 2727 2425
positions_8nt_m1_shift0 (positions_8nt_m1)		0.845	0.528	8.434	0.506	0.913	1.521	0.924	39	109	84	79	78	21	37	63.857	65	; oligos_6nt_mkv4_m2 versus positions_8nt_m1; m=1/1; ncol2=16; w=10; offset=-6; strand=D; shift=0; score=63.8571; amAGATTGCAAAACww ; cor=0.845; Ncor=0.528; logoDP=8.434; NIcor=0.506; NsEucl=0.913; SSD=1.521; NSW=0.924; rcor=39; rNcor=109; rlogoDP=84; rNIcor=79; rNsEucl=78; rSSD=21; rNSW=37; rank_mean=63.857; match_rank=65 a 172 182 482 52 497 2 2 12 3 517 451 522 535 8 215 163 c 112 161 5 27 15 3 0 2 539 6 70 25 3 479 124 119 g 134 132 23 439 22 2 2 518 5 15 2 2 7 22 43 128 t 131 74 39 31 15 542 545 17 2 11 26 0 4 40 167 139

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m4_shift0 (positions_6nt_m4)																		; positions_6nt_m4; m=0 (reference); ncol1=18; shift=0; ncol=18; wsATGTTGCACAACAGtr ; Alignment reference a 39 29 88 5 6 0 1 4 2 115 3 118 117 2 106 5 21 32 c 22 32 16 1 4 0 0 0 114 0 110 0 0 110 2 8 25 29 g 27 31 7 0 106 0 0 110 1 0 1 0 0 3 2 99 25 33 t 30 26 7 112 2 118 117 4 1 3 4 0 1 3 8 6 47 24
positions_7nt_m4_shift0 (positions_7nt_m4)		0.761	0.719	14.244	0.717	0.916	4.061	0.881	101	60	4	36	65	111	94	67.286	69	; positions_6nt_m4 versus positions_7nt_m4; m=1/1; ncol2=17; w=17; offset=0; strand=D; shift=0; score=67.2857; wyCTCTTGCACAACTbh- ; cor=0.761; Ncor=0.719; logoDP=14.244; NIcor=0.717; NsEucl=0.916; SSD=4.061; NSW=0.881; rcor=101; rNcor=60; rlogoDP=4; rNIcor=36; rNsEucl=65; rSSD=111; rNSW=94; rank_mean=67.286; match_rank=69 a 53 47 13 1 20 0 1 2 0 180 11 195 197 3 6 36 50 0 c 42 60 160 8 160 0 0 0 198 8 185 2 1 178 15 53 54 0 g 45 38 9 0 18 0 1 189 1 3 1 1 0 3 3 54 24 0 t 59 54 17 190 1 199 197 8 0 8 2 1 1 15 175 56 71 0

One-to-n matrix alignment; reference matrix: dyads_m3_shift4 ; 4 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m3_shift4 (dyads_m3)																		; dyads_m3; m=0 (reference); ncol1=10; shift=4; ncol=17; ----wdTTGCAAhw--- ; Alignment reference a 0 0 0 0 3278 3895 0 0 0 0 12984 12984 4097 5695 0 0 0 c 0 0 0 0 1633 1516 0 0 0 12984 0 0 3476 2378 0 0 0 g 0 0 0 0 2378 3476 0 0 12984 0 0 0 1516 1633 0 0 0 t 0 0 0 0 5695 4097 12984 12984 0 0 0 0 3895 3278 0 0 0
positions_6nt_m3_shift2 (positions_6nt_m3)		0.822	0.632	11.500	0.602	0.894	2.245	0.888	54	91	49	69	109	49	85	72.286	77	; dyads_m3 versus positions_6nt_m3; m=1/3; ncol2=13; w=10; offset=-2; strand=D; shift=2; score=72.2857; --rmAGTTGCAAAay-- ; cor=0.822; Ncor=0.632; logoDP=11.500; NIcor=0.602; NsEucl=0.894; SSD=2.245; NSW=0.888; rcor=54; rNcor=91; rlogoDP=49; rNIcor=69; rNsEucl=109; rSSD=49; rNSW=85; rank_mean=72.286; match_rank=77 a 0 0 115 113 342 0 0 0 0 0 343 342 344 223 67 0 0 c 0 0 76 100 2 0 0 1 0 344 0 0 0 27 93 0 0 g 0 0 90 71 0 344 0 0 344 0 1 0 0 50 71 0 0 t 0 0 63 60 0 0 344 343 0 0 0 2 0 44 113 0 0
positions_8nt_m1_shift1 (positions_8nt_m1)		0.818	0.511	9.286	0.484	0.898	2.074	0.896	57	110	79	82	104	38	75	77.857	87	; dyads_m3 versus positions_8nt_m1; m=2/3; ncol2=16; w=10; offset=-3; strand=D; shift=1; score=77.8571; -amAGATTGCAAAACww ; cor=0.818; Ncor=0.511; logoDP=9.286; NIcor=0.484; NsEucl=0.898; SSD=2.074; NSW=0.896; rcor=57; rNcor=110; rlogoDP=79; rNIcor=82; rNsEucl=104; rSSD=38; rNSW=75; rank_mean=77.857; match_rank=87 a 0 172 182 482 52 497 2 2 12 3 517 451 522 535 8 215 163 c 0 112 161 5 27 15 3 0 2 539 6 70 25 3 479 124 119 g 0 134 132 23 439 22 2 2 518 5 15 2 2 7 22 43 128 t 0 131 74 39 31 15 542 545 17 2 11 26 0 4 40 167 139
positions_8nt_m5_rc_shift0 (positions_8nt_m5_rc)		0.796	0.468	3.447	0.073	0.890	2.400	0.880	71	111	100	95	110	55	96	91.143	103	; dyads_m3 versus positions_8nt_m5_rc; m=3/3; ncol2=17; w=10; offset=-4; strand=R; shift=0; score=91.1429; waATGATTGCAACATwy ; cor=0.796; Ncor=0.468; logoDP=3.447; NIcor=0.073; NsEucl=0.890; SSD=2.400; NSW=0.880; rcor=71; rNcor=111; rlogoDP=100; rNIcor=95; rNsEucl=110; rSSD=55; rNSW=96; rank_mean=91.143; match_rank=103 a 46 51 134 10 4 157 1 1 6 0 156 144 9 164 1 55 37 c 34 36 10 3 2 3 0 0 1 164 5 2 155 0 7 38 45 g 40 38 13 7 152 3 0 2 152 1 4 3 2 1 4 31 33 t 46 41 9 146 8 3 165 163 7 1 1 17 0 1 154 42 51

One-to-n matrix alignment; reference matrix: dyads_m5_shift2 ; 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_m5_shift2 (dyads_m5)																		; dyads_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --wwCATTTCTbw ; Alignment reference a 0 0 1080 1079 0 3966 0 0 0 0 0 759 1088 c 0 0 830 910 3966 0 0 0 0 3966 0 1011 842 g 0 0 779 741 0 0 0 0 0 0 0 1042 611 t 0 0 1277 1236 0 0 3966 3966 3966 0 3966 1154 1425
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)		0.766	0.648	10.929	0.653	0.895	2.670	0.879	96	84	61	51	108	69	101	81.429	93	; dyads_m5 versus oligos_6nt_mkv4_m4; m=1/1; ncol2=13; w=11; offset=-2; strand=D; shift=0; score=81.4286; ttTTCTTTTCTtt ; cor=0.766; Ncor=0.648; logoDP=10.929; NIcor=0.653; NsEucl=0.895; SSD=2.670; NSW=0.879; rcor=96; rNcor=84; rlogoDP=61; rNIcor=51; rNsEucl=108; rSSD=69; rNSW=101; rank_mean=81.429; match_rank=93 a 284 285 145 199 3 0 6 8 4 1 7 298 281 c 250 209 51 47 1336 0 0 0 1 1338 14 258 292 g 215 182 43 30 0 11 1 0 0 0 46 236 177 t 590 663 1100 1063 0 1328 1332 1331 1334 0 1272 547 589

One-to-n matrix alignment; reference matrix: positions_8nt_m2_shift0 ; 2 matrices ; sort_field=rank_mean

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_8nt_m2_shift0 (positions_8nt_m2)																		; positions_8nt_m2; m=0 (reference); ncol1=16; shift=0; ncol=16; wrTGATTGTGCAAgad ; Alignment reference a 183 173 43 19 589 4 1 23 18 1 24 634 632 19 271 166 c 144 131 13 20 12 4 1 4 12 1 586 4 0 72 129 147 g 140 178 24 576 24 1 10 594 7 632 3 0 4 406 107 165 t 171 156 558 23 13 629 626 17 601 4 25 0 2 141 131 160
positions_8nt_m3_rc_shift2 (positions_8nt_m3_rc)		0.761	0.666	10.211	0.549	0.908	3.329	0.881	102	79	69	76	85	103	92	86.571	101	; positions_8nt_m2 versus positions_8nt_m3_rc; m=1/1; ncol2=14; w=14; offset=2; strand=R; shift=2; score=86.5714; --wtATTGGGCAATaw ; cor=0.761; Ncor=0.666; logoDP=10.211; NIcor=0.549; NsEucl=0.908; SSD=3.329; NSW=0.881; rcor=102; rNcor=79; rlogoDP=69; rNIcor=76; rNsEucl=85; rSSD=103; rNSW=92; rank_mean=86.571; match_rank=101 a 0 0 359 264 809 0 1 12 9 0 2 1115 1117 41 404 311 c 0 0 202 183 80 0 3 4 142 0 1104 1 0 141 258 247 g 0 0 273 259 179 0 4 1097 933 1116 0 1 0 94 210 229 t 0 0 284 412 50 1118 1110 5 34 2 12 1 1 842 246 331