One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $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 -distinct -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m2_shift7 ; 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_shift7 (dyads_test_vs_ctrl_m2)
; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=17; shift=7; ncol=29; -------ssgCCCCGCCCCGCCss----- ; Alignment reference a 0 0 0 0 0 0 0 239 229 121 81 76 79 109 103 58 57 71 96 98 88 97 187 179 0 0 0 0 0 c 0 0 0 0 0 0 0 726 623 262 1223 1188 1203 1191 103 1270 1239 1224 1096 221 1129 1129 679 609 0 0 0 0 0 g 0 0 0 0 0 0 0 407 484 1065 188 222 230 180 1258 182 216 218 256 1138 270 245 451 559 0 0 0 0 0 t 0 0 0 0 0 0 0 210 246 134 90 96 70 102 118 72 70 69 134 125 95 111 265 235 0 0 0 0 0

oligos_7nt_test_vs_ctrl_m3_shift8 (oligos_7nt_test_vs_ctrl_m3) 0.926 0.708 2.581 0.689 0.958 0.593 0.977 2 3 5 2 4 2 2 2.857 1
; dyads_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=1/6; ncol2=13; w=13; offset=1; strand=D; shift=8; score= 2.8571; --------ssCcCCGCCCCss-------- ; cor=0.926; Ncor=0.708; logoDP=2.581; NIcor=0.689; NsEucl=0.958; SSD=0.593; NSW=0.977; rcor=2; rNcor=3; rlogoDP=5; rNIcor=2; rNsEucl=4; rSSD=2; rNSW=2; rank_mean=2.857; match_rank=1 a 0 0 0 0 0 0 0 0 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m1_shift8 (oligos_6nt_test_vs_ctrl_m1) 0.858 0.807 2.369 0.773 0.951 1.252 0.961 8 1 10 1 12 9 9 7.143 5
; dyads_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=2/6; ncol2=16; w=16; offset=1; strand=D; shift=8; score= 7.1429; --------sssgCCGCCCCGCCss----- ; cor=0.858; Ncor=0.807; logoDP=2.369; NIcor=0.773; NsEucl=0.951; SSD=1.252; NSW=0.961; rcor=8; rNcor=1; rlogoDP=10; rNIcor=1; rNsEucl=12; rSSD=9; rNSW=9; rank_mean=7.143; match_rank=5 a 0 0 0 0 0 0 0 0 178 210 115 69 64 74 71 36 50 53 76 63 80 71 162 161 0 0 0 0 0 c 0 0 0 0 0 0 0 0 601 517 356 308 1049 1061 98 1167 1019 1009 1028 156 951 976 568 541 0 0 0 0 0 g 0 0 0 0 0 0 0 0 423 471 827 929 201 178 1129 131 253 246 187 1082 266 251 448 481 0 0 0 0 0 t 0 0 0 0 0 0 0 0 176 180 80 72 64 65 80 44 56 70 87 77 81 80 200 195 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m4_shift5 (oligos_6nt_test_vs_ctrl_m4) 0.867 0.614 1.941 0.588 0.955 1.165 0.966 6 8 18 6 6 7 7 8.286 6
; dyads_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4; m=3/6; ncol2=24; w=17; offset=-2; strand=D; shift=5; score= 8.2857; -----sssssscgCGCCCCGCCCvsssss ; cor=0.867; Ncor=0.614; logoDP=1.941; NIcor=0.588; NsEucl=0.955; SSD=1.165; NSW=0.966; rcor=6; rNcor=8; rlogoDP=18; rNIcor=6; rNsEucl=6; rSSD=7; rNSW=7; rank_mean=8.286; match_rank=6 a 0 0 0 0 0 153 137 120 109 106 88 107 81 62 81 55 67 55 60 59 61 55 35 327 68 105 94 162 157 c 0 0 0 0 0 514 510 621 396 680 723 734 305 887 202 918 840 880 853 158 886 882 934 392 311 313 340 535 476 g 0 0 0 0 0 386 435 329 600 332 316 276 744 207 850 190 239 239 218 941 226 244 200 376 776 732 699 373 418 t 0 0 0 0 0 171 142 154 119 106 97 107 94 68 91 61 78 50 93 66 51 43 55 129 69 74 91 154 173

oligos_6nt_test_vs_ctrl_m5_shift3 (oligos_6nt_test_vs_ctrl_m5) 0.794 0.562 2.277 0.530 0.942 1.949 0.943 20 13 12 11 20 26 23 17.857 19
; dyads_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=4/6; ncol2=24; w=17; offset=-4; strand=D; shift=3; score=17.8571; ---sssccvGCCCCGCCCCvGggCsss-- ; cor=0.794; Ncor=0.562; logoDP=2.277; NIcor=0.530; NsEucl=0.942; SSD=1.949; NSW=0.943; rcor=20; rNcor=13; rlogoDP=12; rNIcor=11; rNsEucl=20; rSSD=26; rNSW=23; rank_mean=17.857; match_rank=19 a 0 0 0 101 91 46 48 64 205 39 44 46 29 40 40 34 20 22 35 240 35 49 49 33 143 74 96 0 0 c 0 0 0 259 251 165 424 440 198 107 499 457 487 472 43 489 506 494 485 168 110 146 147 514 218 261 255 0 0 g 0 0 0 195 204 376 135 119 177 461 84 110 94 82 528 103 97 91 106 187 482 429 421 71 203 236 214 0 0 t 0 0 0 98 107 66 46 30 73 46 26 40 43 59 42 27 30 46 27 58 26 29 36 35 89 82 88 0 0

dyads_test_vs_ctrl_m4_shift0 (dyads_test_vs_ctrl_m4) 0.789 0.427 1.187 0.419 0.934 1.469 0.943 21 27 24 22 25 18 22 22.714 26
; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m4; m=5/6; ncol2=20; w=13; offset=-7; strand=D; shift=0; score=22.7143; ssGGCssssssssssCCCss--------- ; cor=0.789; Ncor=0.427; logoDP=1.187; NIcor=0.419; NsEucl=0.934; SSD=1.469; NSW=0.943; rcor=21; rNcor=27; rlogoDP=24; rNIcor=22; rNsEucl=25; rSSD=18; rNSW=22; rank_mean=22.714; match_rank=26 a 380 415 136 98 92 249 206 50 520 359 261 57 59 391 91 143 143 134 366 335 0 0 0 0 0 0 0 0 0 c 1221 1138 533 373 2485 1396 1251 1519 1054 1112 1102 1381 1463 1386 1250 2007 2001 2038 1031 971 0 0 0 0 0 0 0 0 0 g 939 962 2082 2291 229 927 961 1233 1255 1368 1473 1198 1030 1031 1440 584 582 543 1039 1212 0 0 0 0 0 0 0 0 0 t 345 370 134 123 79 313 467 83 56 46 49 249 333 77 104 151 159 170 449 367 0 0 0 0 0 0 0 0 0

dyads_test_vs_ctrl_m5_rc_shift7 (dyads_test_vs_ctrl_m5_rc) 0.756 0.443 0.995 0.205 0.942 1.967 0.942 29 24 28 28 21 27 24 25.857 29
; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m5_rc; m=6/6; ncol2=29; w=17; offset=0; strand=R; shift=7; score=25.8571; -------ssgccssgssssssssssssss ; cor=0.756; Ncor=0.443; logoDP=0.995; NIcor=0.205; NsEucl=0.942; SSD=1.967; NSW=0.942; rcor=29; rNcor=24; rlogoDP=28; rNIcor=28; rNsEucl=21; rSSD=27; rNSW=24; rank_mean=25.857; match_rank=29 a 0 0 0 0 0 0 0 440 448 226 209 237 368 384 253 171 161 154 125 130 143 137 149 126 124 109 114 161 569 c 0 0 0 0 0 0 0 1439 1289 797 2304 2218 1425 1393 861 1516 1692 1709 1720 1582 1405 1465 1566 1563 1728 1711 1491 1570 1293 g 0 0 0 0 0 0 0 1243 1347 2261 790 811 1306 1356 2180 1700 1538 1492 1517 1385 1580 1773 1704 1731 1304 1288 1387 1688 1573 t 0 0 0 0 0 0 0 425 463 263 244 281 448 414 253 160 156 192 185 450 419 172 128 127 391 439 555 128 112

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_shift7 (dyads_test_vs_ctrl_m2)																	; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=17; shift=7; ncol=29; -------ssgCCCCGCCCCGCCss----- ; Alignment reference a 0 0 0 0 0 0 0 239 229 121 81 76 79 109 103 58 57 71 96 98 88 97 187 179 0 0 0 0 0 c 0 0 0 0 0 0 0 726 623 262 1223 1188 1203 1191 103 1270 1239 1224 1096 221 1129 1129 679 609 0 0 0 0 0 g 0 0 0 0 0 0 0 407 484 1065 188 222 230 180 1258 182 216 218 256 1138 270 245 451 559 0 0 0 0 0 t 0 0 0 0 0 0 0 210 246 134 90 96 70 102 118 72 70 69 134 125 95 111 265 235 0 0 0 0 0
oligos_7nt_test_vs_ctrl_m3_shift8 (oligos_7nt_test_vs_ctrl_m3)	0.926	0.708	2.581	0.689	0.958	0.593	0.977	2	3	5	2	4	2	2	2.857	1	; dyads_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=1/6; ncol2=13; w=13; offset=1; strand=D; shift=8; score= 2.8571; --------ssCcCCGCCCCss-------- ; cor=0.926; Ncor=0.708; logoDP=2.581; NIcor=0.689; NsEucl=0.958; SSD=0.593; NSW=0.977; rcor=2; rNcor=3; rlogoDP=5; rNIcor=2; rNsEucl=4; rSSD=2; rNSW=2; rank_mean=2.857; match_rank=1 a 0 0 0 0 0 0 0 0 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m1_shift8 (oligos_6nt_test_vs_ctrl_m1)	0.858	0.807	2.369	0.773	0.951	1.252	0.961	8	1	10	1	12	9	9	7.143	5	; dyads_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=2/6; ncol2=16; w=16; offset=1; strand=D; shift=8; score= 7.1429; --------sssgCCGCCCCGCCss----- ; cor=0.858; Ncor=0.807; logoDP=2.369; NIcor=0.773; NsEucl=0.951; SSD=1.252; NSW=0.961; rcor=8; rNcor=1; rlogoDP=10; rNIcor=1; rNsEucl=12; rSSD=9; rNSW=9; rank_mean=7.143; match_rank=5 a 0 0 0 0 0 0 0 0 178 210 115 69 64 74 71 36 50 53 76 63 80 71 162 161 0 0 0 0 0 c 0 0 0 0 0 0 0 0 601 517 356 308 1049 1061 98 1167 1019 1009 1028 156 951 976 568 541 0 0 0 0 0 g 0 0 0 0 0 0 0 0 423 471 827 929 201 178 1129 131 253 246 187 1082 266 251 448 481 0 0 0 0 0 t 0 0 0 0 0 0 0 0 176 180 80 72 64 65 80 44 56 70 87 77 81 80 200 195 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m4_shift5 (oligos_6nt_test_vs_ctrl_m4)	0.867	0.614	1.941	0.588	0.955	1.165	0.966	6	8	18	6	6	7	7	8.286	6	; dyads_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4; m=3/6; ncol2=24; w=17; offset=-2; strand=D; shift=5; score= 8.2857; -----sssssscgCGCCCCGCCCvsssss ; cor=0.867; Ncor=0.614; logoDP=1.941; NIcor=0.588; NsEucl=0.955; SSD=1.165; NSW=0.966; rcor=6; rNcor=8; rlogoDP=18; rNIcor=6; rNsEucl=6; rSSD=7; rNSW=7; rank_mean=8.286; match_rank=6 a 0 0 0 0 0 153 137 120 109 106 88 107 81 62 81 55 67 55 60 59 61 55 35 327 68 105 94 162 157 c 0 0 0 0 0 514 510 621 396 680 723 734 305 887 202 918 840 880 853 158 886 882 934 392 311 313 340 535 476 g 0 0 0 0 0 386 435 329 600 332 316 276 744 207 850 190 239 239 218 941 226 244 200 376 776 732 699 373 418 t 0 0 0 0 0 171 142 154 119 106 97 107 94 68 91 61 78 50 93 66 51 43 55 129 69 74 91 154 173
oligos_6nt_test_vs_ctrl_m5_shift3 (oligos_6nt_test_vs_ctrl_m5)	0.794	0.562	2.277	0.530	0.942	1.949	0.943	20	13	12	11	20	26	23	17.857	19	; dyads_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=4/6; ncol2=24; w=17; offset=-4; strand=D; shift=3; score=17.8571; ---sssccvGCCCCGCCCCvGggCsss-- ; cor=0.794; Ncor=0.562; logoDP=2.277; NIcor=0.530; NsEucl=0.942; SSD=1.949; NSW=0.943; rcor=20; rNcor=13; rlogoDP=12; rNIcor=11; rNsEucl=20; rSSD=26; rNSW=23; rank_mean=17.857; match_rank=19 a 0 0 0 101 91 46 48 64 205 39 44 46 29 40 40 34 20 22 35 240 35 49 49 33 143 74 96 0 0 c 0 0 0 259 251 165 424 440 198 107 499 457 487 472 43 489 506 494 485 168 110 146 147 514 218 261 255 0 0 g 0 0 0 195 204 376 135 119 177 461 84 110 94 82 528 103 97 91 106 187 482 429 421 71 203 236 214 0 0 t 0 0 0 98 107 66 46 30 73 46 26 40 43 59 42 27 30 46 27 58 26 29 36 35 89 82 88 0 0
dyads_test_vs_ctrl_m4_shift0 (dyads_test_vs_ctrl_m4)	0.789	0.427	1.187	0.419	0.934	1.469	0.943	21	27	24	22	25	18	22	22.714	26	; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m4; m=5/6; ncol2=20; w=13; offset=-7; strand=D; shift=0; score=22.7143; ssGGCssssssssssCCCss--------- ; cor=0.789; Ncor=0.427; logoDP=1.187; NIcor=0.419; NsEucl=0.934; SSD=1.469; NSW=0.943; rcor=21; rNcor=27; rlogoDP=24; rNIcor=22; rNsEucl=25; rSSD=18; rNSW=22; rank_mean=22.714; match_rank=26 a 380 415 136 98 92 249 206 50 520 359 261 57 59 391 91 143 143 134 366 335 0 0 0 0 0 0 0 0 0 c 1221 1138 533 373 2485 1396 1251 1519 1054 1112 1102 1381 1463 1386 1250 2007 2001 2038 1031 971 0 0 0 0 0 0 0 0 0 g 939 962 2082 2291 229 927 961 1233 1255 1368 1473 1198 1030 1031 1440 584 582 543 1039 1212 0 0 0 0 0 0 0 0 0 t 345 370 134 123 79 313 467 83 56 46 49 249 333 77 104 151 159 170 449 367 0 0 0 0 0 0 0 0 0
dyads_test_vs_ctrl_m5_rc_shift7 (dyads_test_vs_ctrl_m5_rc)	0.756	0.443	0.995	0.205	0.942	1.967	0.942	29	24	28	28	21	27	24	25.857	29	; dyads_test_vs_ctrl_m2 versus dyads_test_vs_ctrl_m5_rc; m=6/6; ncol2=29; w=17; offset=0; strand=R; shift=7; score=25.8571; -------ssgccssgssssssssssssss ; cor=0.756; Ncor=0.443; logoDP=0.995; NIcor=0.205; NsEucl=0.942; SSD=1.967; NSW=0.942; rcor=29; rNcor=24; rlogoDP=28; rNIcor=28; rNsEucl=21; rSSD=27; rNSW=24; rank_mean=25.857; match_rank=29 a 0 0 0 0 0 0 0 440 448 226 209 237 368 384 253 171 161 154 125 130 143 137 149 126 124 109 114 161 569 c 0 0 0 0 0 0 0 1439 1289 797 2304 2218 1425 1393 861 1516 1692 1709 1720 1582 1405 1465 1566 1563 1728 1711 1491 1570 1293 g 0 0 0 0 0 0 0 1243 1347 2261 790 811 1306 1356 2180 1700 1538 1492 1517 1385 1580 1773 1704 1731 1304 1288 1387 1688 1573 t 0 0 0 0 0 0 0 425 463 263 244 281 448 414 253 160 156 192 185 450 419 172 128 127 391 439 555 128 112

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift5 ; 5 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift5 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=22; shift=5; ncol=30; -----ssgGCCGCCCCvGGGCaGggss--- ; Alignment reference a 0 0 0 0 0 73 101 58 47 39 62 35 31 26 34 32 259 23 37 32 34 286 34 57 47 105 99 0 0 0 c 0 0 0 0 0 232 218 132 107 468 431 48 473 444 446 463 161 73 112 97 492 129 105 129 139 237 178 0 0 0 g 0 0 0 0 0 235 207 371 430 84 79 498 82 104 96 96 166 505 442 457 74 147 443 390 370 197 241 0 0 0 t 0 0 0 0 0 79 93 58 35 28 47 38 33 45 43 28 33 18 28 33 19 57 37 43 63 80 101 0 0 0

oligos_7nt_test_vs_ctrl_m1_shift9 (oligos_7nt_test_vs_ctrl_m1) 0.902 0.574 2.904 0.554 0.954 0.846 0.970 4 11 3 7 8 5 4 6.000 2
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=1/4; ncol2=14; w=14; offset=4; strand=D; shift=9; score= 6; ---------csGCCCCaGGgcss------- ; cor=0.902; Ncor=0.574; logoDP=2.904; NIcor=0.554; NsEucl=0.954; SSD=0.846; NSW=0.970; rcor=4; rNcor=11; rlogoDP=3; rNIcor=7; rNsEucl=8; rSSD=5; rNSW=4; rank_mean=6.000; match_rank=2 a 0 0 0 0 0 0 0 0 0 195 244 54 37 19 21 11 808 21 17 123 132 281 174 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 548 431 70 1140 1083 1093 1108 179 89 101 283 849 359 410 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 314 350 1071 58 138 117 132 248 1147 1134 747 185 425 448 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 210 242 72 32 27 36 16 32 10 15 114 101 202 235 0 0 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5) 0.817 0.575 2.375 0.548 0.950 1.774 0.953 14 10 9 9 13 21 14 12.857 12
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=2/4; ncol2=24; w=19; offset=-5; strand=D; shift=0; score=12.8571; sssccvGCCCCGCCCCvGggCsss------ ; cor=0.817; Ncor=0.575; logoDP=2.375; NIcor=0.548; NsEucl=0.950; SSD=1.774; NSW=0.953; rcor=14; rNcor=10; rlogoDP=9; rNIcor=9; rNsEucl=13; rSSD=21; rNSW=14; rank_mean=12.857; match_rank=12 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 0 0 0 0 0 0 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 0 0 0 0 0 0 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 0 0 0 0 0 0 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 0 0 0 0 0 0

oligos_7nt_test_vs_ctrl_m3_shift5 (oligos_7nt_test_vs_ctrl_m3) 0.812 0.480 2.132 0.456 0.936 1.386 0.947 16 20 13 18 23 14 21 17.857 20
; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=3/4; ncol2=13; w=13; offset=0; strand=D; shift=5; score=17.8571; -----ssCcCCGCCCCss------------ ; cor=0.812; Ncor=0.480; logoDP=2.132; NIcor=0.456; NsEucl=0.936; SSD=1.386; NSW=0.947; rcor=16; rNcor=20; rlogoDP=13; rNIcor=18; rNsEucl=23; rSSD=14; rNSW=21; rank_mean=17.857; match_rank=20 a 0 0 0 0 0 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0 0 0 0 0 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m4_rc_shift11 (oligos_6nt_test_vs_ctrl_m4_rc) 0.811 0.433 0.744 0.027 0.946 1.493 0.953 17 25 29 29 16 19 13 21.143 23
; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=4/4; ncol2=24; w=16; offset=6; strand=R; shift=11; score=21.1429; -----------sssssbGGGCGGGGCGcgs ; cor=0.811; Ncor=0.433; logoDP=0.744; NIcor=0.027; NsEucl=0.946; SSD=1.493; NSW=0.953; rcor=17; rNcor=25; rlogoDP=29; rNIcor=29; rNsEucl=16; rSSD=19; rNSW=13; rank_mean=21.143; match_rank=23 a 0 0 0 0 0 0 0 0 0 0 0 173 154 91 74 69 129 55 43 51 66 93 50 78 61 91 68 94 107 97 c 0 0 0 0 0 0 0 0 0 0 0 418 373 699 732 776 376 200 244 226 941 218 239 239 190 850 207 744 276 316 g 0 0 0 0 0 0 0 0 0 0 0 476 535 340 313 311 392 934 882 886 158 853 880 840 918 202 887 305 734 723 t 0 0 0 0 0 0 0 0 0 0 0 157 162 94 105 68 327 35 55 61 59 60 55 67 55 81 62 81 107 88

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_test_vs_ctrl_m2_shift5 (oligos_6nt_test_vs_ctrl_m2)																	; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=22; shift=5; ncol=30; -----ssgGCCGCCCCvGGGCaGggss--- ; Alignment reference a 0 0 0 0 0 73 101 58 47 39 62 35 31 26 34 32 259 23 37 32 34 286 34 57 47 105 99 0 0 0 c 0 0 0 0 0 232 218 132 107 468 431 48 473 444 446 463 161 73 112 97 492 129 105 129 139 237 178 0 0 0 g 0 0 0 0 0 235 207 371 430 84 79 498 82 104 96 96 166 505 442 457 74 147 443 390 370 197 241 0 0 0 t 0 0 0 0 0 79 93 58 35 28 47 38 33 45 43 28 33 18 28 33 19 57 37 43 63 80 101 0 0 0
oligos_7nt_test_vs_ctrl_m1_shift9 (oligos_7nt_test_vs_ctrl_m1)	0.902	0.574	2.904	0.554	0.954	0.846	0.970	4	11	3	7	8	5	4	6.000	2	; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m1; m=1/4; ncol2=14; w=14; offset=4; strand=D; shift=9; score= 6; ---------csGCCCCaGGgcss------- ; cor=0.902; Ncor=0.574; logoDP=2.904; NIcor=0.554; NsEucl=0.954; SSD=0.846; NSW=0.970; rcor=4; rNcor=11; rlogoDP=3; rNIcor=7; rNsEucl=8; rSSD=5; rNSW=4; rank_mean=6.000; match_rank=2 a 0 0 0 0 0 0 0 0 0 195 244 54 37 19 21 11 808 21 17 123 132 281 174 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 548 431 70 1140 1083 1093 1108 179 89 101 283 849 359 410 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 314 350 1071 58 138 117 132 248 1147 1134 747 185 425 448 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 210 242 72 32 27 36 16 32 10 15 114 101 202 235 0 0 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)	0.817	0.575	2.375	0.548	0.950	1.774	0.953	14	10	9	9	13	21	14	12.857	12	; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=2/4; ncol2=24; w=19; offset=-5; strand=D; shift=0; score=12.8571; sssccvGCCCCGCCCCvGggCsss------ ; cor=0.817; Ncor=0.575; logoDP=2.375; NIcor=0.548; NsEucl=0.950; SSD=1.774; NSW=0.953; rcor=14; rNcor=10; rlogoDP=9; rNIcor=9; rNsEucl=13; rSSD=21; rNSW=14; rank_mean=12.857; match_rank=12 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 0 0 0 0 0 0 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 0 0 0 0 0 0 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 0 0 0 0 0 0 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 0 0 0 0 0 0
oligos_7nt_test_vs_ctrl_m3_shift5 (oligos_7nt_test_vs_ctrl_m3)	0.812	0.480	2.132	0.456	0.936	1.386	0.947	16	20	13	18	23	14	21	17.857	20	; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3; m=3/4; ncol2=13; w=13; offset=0; strand=D; shift=5; score=17.8571; -----ssCcCCGCCCCss------------ ; cor=0.812; Ncor=0.480; logoDP=2.132; NIcor=0.456; NsEucl=0.936; SSD=1.386; NSW=0.947; rcor=16; rNcor=20; rlogoDP=13; rNIcor=18; rNsEucl=23; rSSD=14; rNSW=21; rank_mean=17.857; match_rank=20 a 0 0 0 0 0 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0 0 0 0 0 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m4_rc_shift11 (oligos_6nt_test_vs_ctrl_m4_rc)	0.811	0.433	0.744	0.027	0.946	1.493	0.953	17	25	29	29	16	19	13	21.143	23	; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m4_rc; m=4/4; ncol2=24; w=16; offset=6; strand=R; shift=11; score=21.1429; -----------sssssbGGGCGGGGCGcgs ; cor=0.811; Ncor=0.433; logoDP=0.744; NIcor=0.027; NsEucl=0.946; SSD=1.493; NSW=0.953; rcor=17; rNcor=25; rlogoDP=29; rNIcor=29; rNsEucl=16; rSSD=19; rNSW=13; rank_mean=21.143; match_rank=23 a 0 0 0 0 0 0 0 0 0 0 0 173 154 91 74 69 129 55 43 51 66 93 50 78 61 91 68 94 107 97 c 0 0 0 0 0 0 0 0 0 0 0 418 373 699 732 776 376 200 244 226 941 218 239 239 190 850 207 744 276 316 g 0 0 0 0 0 0 0 0 0 0 0 476 535 340 313 311 392 934 882 886 158 853 880 840 918 202 887 305 734 723 t 0 0 0 0 0 0 0 0 0 0 0 157 162 94 105 68 327 35 55 61 59 60 55 67 55 81 62 81 107 88

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

oligos_7nt_test_vs_ctrl_m1_shift9 (oligos_7nt_test_vs_ctrl_m1) 0.921 0.537 2.756 0.521 0.959 0.671 0.976 3 16 4 13 3 3 3 6.429 3
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=1/2; ncol2=14; w=14; offset=9; strand=D; shift=9; score= 6.4286; ---------csGCCCCaGGgcss- ; cor=0.921; Ncor=0.537; logoDP=2.756; NIcor=0.521; NsEucl=0.959; SSD=0.671; NSW=0.976; rcor=3; rNcor=16; rlogoDP=4; rNIcor=13; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=6.429; match_rank=3 a 0 0 0 0 0 0 0 0 0 195 244 54 37 19 21 11 808 21 17 123 132 281 174 0 c 0 0 0 0 0 0 0 0 0 548 431 70 1140 1083 1093 1108 179 89 101 283 849 359 410 0 g 0 0 0 0 0 0 0 0 0 314 350 1071 58 138 117 132 248 1147 1134 747 185 425 448 0 t 0 0 0 0 0 0 0 0 0 210 242 72 32 27 36 16 32 10 15 114 101 202 235 0

oligos_7nt_test_vs_ctrl_m3_shift5 (oligos_7nt_test_vs_ctrl_m3) 0.930 0.504 2.461 0.497 0.960 0.536 0.979 1 17 8 15 2 1 1 6.429 4
; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3; m=2/2; ncol2=13; w=13; offset=5; strand=D; shift=5; score= 6.4286; -----ssCcCCGCCCCss------ ; cor=0.930; Ncor=0.504; logoDP=2.461; NIcor=0.497; NsEucl=0.960; SSD=0.536; NSW=0.979; rcor=1; rNcor=17; rlogoDP=8; rNIcor=15; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=6.429; match_rank=4 a 0 0 0 0 0 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 0 0 0 c 0 0 0 0 0 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 0 0 0 g 0 0 0 0 0 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 0 0 0 t 0 0 0 0 0 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_test_vs_ctrl_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
oligos_7nt_test_vs_ctrl_m1_shift9 (oligos_7nt_test_vs_ctrl_m1)	0.921	0.537	2.756	0.521	0.959	0.671	0.976	3	16	4	13	3	3	3	6.429	3	; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=1/2; ncol2=14; w=14; offset=9; strand=D; shift=9; score= 6.4286; ---------csGCCCCaGGgcss- ; cor=0.921; Ncor=0.537; logoDP=2.756; NIcor=0.521; NsEucl=0.959; SSD=0.671; NSW=0.976; rcor=3; rNcor=16; rlogoDP=4; rNIcor=13; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=6.429; match_rank=3 a 0 0 0 0 0 0 0 0 0 195 244 54 37 19 21 11 808 21 17 123 132 281 174 0 c 0 0 0 0 0 0 0 0 0 548 431 70 1140 1083 1093 1108 179 89 101 283 849 359 410 0 g 0 0 0 0 0 0 0 0 0 314 350 1071 58 138 117 132 248 1147 1134 747 185 425 448 0 t 0 0 0 0 0 0 0 0 0 210 242 72 32 27 36 16 32 10 15 114 101 202 235 0
oligos_7nt_test_vs_ctrl_m3_shift5 (oligos_7nt_test_vs_ctrl_m3)	0.930	0.504	2.461	0.497	0.960	0.536	0.979	1	17	8	15	2	1	1	6.429	4	; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3; m=2/2; ncol2=13; w=13; offset=5; strand=D; shift=5; score= 6.4286; -----ssCcCCGCCCCss------ ; cor=0.930; Ncor=0.504; logoDP=2.461; NIcor=0.497; NsEucl=0.960; SSD=0.536; NSW=0.979; rcor=1; rNcor=17; rlogoDP=8; rNIcor=15; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=6.429; match_rank=4 a 0 0 0 0 0 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 0 0 0 c 0 0 0 0 0 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 0 0 0 g 0 0 0 0 0 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 0 0 0 t 0 0 0 0 0 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift3 ; 4 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_6nt_test_vs_ctrl_m1_shift3 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=16; shift=3; ncol=24; ---sssgCCGCCCCGCCss----- ; Alignment reference a 0 0 0 178 210 115 69 64 74 71 36 50 53 76 63 80 71 162 161 0 0 0 0 0 c 0 0 0 601 517 356 308 1049 1061 98 1167 1019 1009 1028 156 951 976 568 541 0 0 0 0 0 g 0 0 0 423 471 827 929 201 178 1129 131 253 246 187 1082 266 251 448 481 0 0 0 0 0 t 0 0 0 176 180 80 72 64 65 80 44 56 70 87 77 81 80 200 195 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m5_shift3 (oligos_6nt_test_vs_ctrl_m5) 0.866 0.577 2.009 0.549 0.953 1.119 0.965 7 9 16 8 9 6 8 9.000 7
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=1/3; ncol2=24; w=16; offset=0; strand=D; shift=3; score= 9; ---sssccvGCCCCGCCCCvGggC ; cor=0.866; Ncor=0.577; logoDP=2.009; NIcor=0.549; NsEucl=0.953; SSD=1.119; NSW=0.965; rcor=7; rNcor=9; rlogoDP=16; rNIcor=8; rNsEucl=9; rSSD=6; rNSW=8; rank_mean=9.000; match_rank=7 a 0 0 0 101 91 46 48 64 205 39 44 46 29 40 40 34 20 22 35 240 35 49 49 33 c 0 0 0 259 251 165 424 440 198 107 499 457 487 472 43 489 506 494 485 168 110 146 147 514 g 0 0 0 195 204 376 135 119 177 461 84 110 94 82 528 103 97 91 106 187 482 429 421 71 t 0 0 0 98 107 66 46 30 73 46 26 40 43 59 42 27 30 46 27 58 26 29 36 35

oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3) 0.835 0.678 2.544 0.639 0.939 1.278 0.951 10 4 7 4 22 10 19 10.857 9
; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=2/3; ncol2=13; w=13; offset=0; strand=D; shift=3; score=10.8571; ---ssCcCCGCCCCss-------- ; cor=0.835; Ncor=0.678; logoDP=2.544; NIcor=0.639; NsEucl=0.939; SSD=1.278; NSW=0.951; rcor=10; rNcor=4; rlogoDP=7; rNIcor=4; rNsEucl=22; rSSD=10; rNSW=19; rank_mean=10.857; match_rank=9 a 0 0 0 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 0 0 0 0 0 c 0 0 0 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 0 0 0 0 0 g 0 0 0 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 0 0 0 0 0 t 0 0 0 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4) 0.830 0.554 1.949 0.517 0.948 1.395 0.956 11 14 17 14 15 15 10 13.714 14
; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=3/3; ncol2=24; w=16; offset=-3; strand=D; shift=0; score=13.7143; sssssscgCGCCCCGCCCvsssss ; cor=0.830; Ncor=0.554; logoDP=1.949; NIcor=0.517; NsEucl=0.948; SSD=1.395; NSW=0.956; rcor=11; rNcor=14; rlogoDP=17; rNIcor=14; rNsEucl=15; rSSD=15; rNSW=10; rank_mean=13.714; match_rank=14 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

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_shift3 (oligos_6nt_test_vs_ctrl_m1)																	; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=16; shift=3; ncol=24; ---sssgCCGCCCCGCCss----- ; Alignment reference a 0 0 0 178 210 115 69 64 74 71 36 50 53 76 63 80 71 162 161 0 0 0 0 0 c 0 0 0 601 517 356 308 1049 1061 98 1167 1019 1009 1028 156 951 976 568 541 0 0 0 0 0 g 0 0 0 423 471 827 929 201 178 1129 131 253 246 187 1082 266 251 448 481 0 0 0 0 0 t 0 0 0 176 180 80 72 64 65 80 44 56 70 87 77 81 80 200 195 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m5_shift3 (oligos_6nt_test_vs_ctrl_m5)	0.866	0.577	2.009	0.549	0.953	1.119	0.965	7	9	16	8	9	6	8	9.000	7	; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m5; m=1/3; ncol2=24; w=16; offset=0; strand=D; shift=3; score= 9; ---sssccvGCCCCGCCCCvGggC ; cor=0.866; Ncor=0.577; logoDP=2.009; NIcor=0.549; NsEucl=0.953; SSD=1.119; NSW=0.965; rcor=7; rNcor=9; rlogoDP=16; rNIcor=8; rNsEucl=9; rSSD=6; rNSW=8; rank_mean=9.000; match_rank=7 a 0 0 0 101 91 46 48 64 205 39 44 46 29 40 40 34 20 22 35 240 35 49 49 33 c 0 0 0 259 251 165 424 440 198 107 499 457 487 472 43 489 506 494 485 168 110 146 147 514 g 0 0 0 195 204 376 135 119 177 461 84 110 94 82 528 103 97 91 106 187 482 429 421 71 t 0 0 0 98 107 66 46 30 73 46 26 40 43 59 42 27 30 46 27 58 26 29 36 35
oligos_7nt_test_vs_ctrl_m3_shift3 (oligos_7nt_test_vs_ctrl_m3)	0.835	0.678	2.544	0.639	0.939	1.278	0.951	10	4	7	4	22	10	19	10.857	9	; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=2/3; ncol2=13; w=13; offset=0; strand=D; shift=3; score=10.8571; ---ssCcCCGCCCCss-------- ; cor=0.835; Ncor=0.678; logoDP=2.544; NIcor=0.639; NsEucl=0.939; SSD=1.278; NSW=0.951; rcor=10; rNcor=4; rlogoDP=7; rNIcor=4; rNsEucl=22; rSSD=10; rNSW=19; rank_mean=10.857; match_rank=9 a 0 0 0 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 0 0 0 0 0 c 0 0 0 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 0 0 0 0 0 g 0 0 0 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 0 0 0 0 0 t 0 0 0 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)	0.830	0.554	1.949	0.517	0.948	1.395	0.956	11	14	17	14	15	15	10	13.714	14	; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m4; m=3/3; ncol2=24; w=16; offset=-3; strand=D; shift=0; score=13.7143; sssssscgCGCCCCGCCCvsssss ; cor=0.830; Ncor=0.554; logoDP=1.949; NIcor=0.517; NsEucl=0.948; SSD=1.395; NSW=0.956; rcor=11; rNcor=14; rlogoDP=17; rNIcor=14; rNsEucl=15; rSSD=15; rNSW=10; rank_mean=13.714; match_rank=14 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

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_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_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)
; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=0; ncol=27; 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 0 0 0 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 0 0 0 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 0 0 0 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 0 0 0

oligos_7nt_test_vs_ctrl_m3_shift8 (oligos_7nt_test_vs_ctrl_m3) 0.894 0.484 2.101 0.463 0.951 0.801 0.969 5 19 14 17 11 4 6 10.857 8
; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=1/2; ncol2=13; w=13; offset=8; strand=D; shift=8; score=10.8571; --------ssCcCCGCCCCss------ ; cor=0.894; Ncor=0.484; logoDP=2.101; NIcor=0.463; NsEucl=0.951; SSD=0.801; NSW=0.969; rcor=5; rNcor=19; rlogoDP=14; rNIcor=17; rNsEucl=11; rSSD=4; rNSW=6; rank_mean=10.857; match_rank=8 a 0 0 0 0 0 0 0 0 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m5_shift3 (oligos_6nt_test_vs_ctrl_m5) 0.815 0.634 2.067 0.599 0.954 1.860 0.956 15 6 15 5 7 22 12 11.714 11
; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=2/2; ncol2=24; w=21; offset=3; strand=D; shift=3; score=11.7143; ---sssccvGCCCCGCCCCvGggCsss ; cor=0.815; Ncor=0.634; logoDP=2.067; NIcor=0.599; NsEucl=0.954; SSD=1.860; NSW=0.956; rcor=15; rNcor=6; rlogoDP=15; rNIcor=5; rNsEucl=7; rSSD=22; rNSW=12; rank_mean=11.714; match_rank=11 a 0 0 0 101 91 46 48 64 205 39 44 46 29 40 40 34 20 22 35 240 35 49 49 33 143 74 96 c 0 0 0 259 251 165 424 440 198 107 499 457 487 472 43 489 506 494 485 168 110 146 147 514 218 261 255 g 0 0 0 195 204 376 135 119 177 461 84 110 94 82 528 103 97 91 106 187 482 429 421 71 203 236 214 t 0 0 0 98 107 66 46 30 73 46 26 40 43 59 42 27 30 46 27 58 26 29 36 35 89 82 88

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4)																	; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=0; ncol=27; 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 0 0 0 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 0 0 0 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 0 0 0 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 0 0 0
oligos_7nt_test_vs_ctrl_m3_shift8 (oligos_7nt_test_vs_ctrl_m3)	0.894	0.484	2.101	0.463	0.951	0.801	0.969	5	19	14	17	11	4	6	10.857	8	; oligos_6nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=1/2; ncol2=13; w=13; offset=8; strand=D; shift=8; score=10.8571; --------ssCcCCGCCCCss------ ; cor=0.894; Ncor=0.484; logoDP=2.101; NIcor=0.463; NsEucl=0.951; SSD=0.801; NSW=0.969; rcor=5; rNcor=19; rlogoDP=14; rNIcor=17; rNsEucl=11; rSSD=4; rNSW=6; rank_mean=10.857; match_rank=8 a 0 0 0 0 0 0 0 0 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m5_shift3 (oligos_6nt_test_vs_ctrl_m5)	0.815	0.634	2.067	0.599	0.954	1.860	0.956	15	6	15	5	7	22	12	11.714	11	; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m5; m=2/2; ncol2=24; w=21; offset=3; strand=D; shift=3; score=11.7143; ---sssccvGCCCCGCCCCvGggCsss ; cor=0.815; Ncor=0.634; logoDP=2.067; NIcor=0.599; NsEucl=0.954; SSD=1.860; NSW=0.956; rcor=15; rNcor=6; rlogoDP=15; rNIcor=5; rNsEucl=7; rSSD=22; rNSW=12; rank_mean=11.714; match_rank=11 a 0 0 0 101 91 46 48 64 205 39 44 46 29 40 40 34 20 22 35 240 35 49 49 33 143 74 96 c 0 0 0 259 251 165 424 440 198 107 499 457 487 472 43 489 506 494 485 168 110 146 147 514 218 261 255 g 0 0 0 195 204 376 135 119 177 461 84 110 94 82 528 103 97 91 106 187 482 429 421 71 203 236 214 t 0 0 0 98 107 66 46 30 73 46 26 40 43 59 42 27 30 46 27 58 26 29 36 35 89 82 88

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_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
dyads_test_vs_ctrl_m4_shift1 (dyads_test_vs_ctrl_m4)
; dyads_test_vs_ctrl_m4; m=0 (reference); ncol1=20; shift=1; ncol=29; -ssGGCssssssssssCCCss-------- ; Alignment reference a 0 380 415 136 98 92 249 206 50 520 359 261 57 59 391 91 143 143 134 366 335 0 0 0 0 0 0 0 0 c 0 1221 1138 533 373 2485 1396 1251 1519 1054 1112 1102 1381 1463 1386 1250 2007 2001 2038 1031 971 0 0 0 0 0 0 0 0 g 0 939 962 2082 2291 229 927 961 1233 1255 1368 1473 1198 1030 1031 1440 584 582 543 1039 1212 0 0 0 0 0 0 0 0 t 0 345 370 134 123 79 313 467 83 56 46 49 249 333 77 104 151 159 170 449 367 0 0 0 0 0 0 0 0

dyads_test_vs_ctrl_m5_shift0 (dyads_test_vs_ctrl_m5) 0.826 0.570 1.146 0.480 0.961 1.210 0.970 12 12 25 16 1 8 5 11.286 10
; dyads_test_vs_ctrl_m4 versus dyads_test_vs_ctrl_m5; m=1/4; ncol2=29; w=20; offset=-1; strand=D; shift=0; score=11.2857; sscvGsssssssssssssssscssggcss ; cor=0.826; Ncor=0.570; logoDP=1.146; NIcor=0.480; NsEucl=0.961; SSD=1.210; NSW=0.970; rcor=12; rNcor=12; rlogoDP=25; rNIcor=16; rNsEucl=1; rSSD=8; rNSW=5; rank_mean=11.286; match_rank=10 a 425 389 218 1033 168 134 106 112 128 555 439 391 127 128 172 419 450 185 192 156 160 253 414 448 281 244 263 463 425 c 1472 1338 2342 1063 691 1843 1779 1573 1688 1387 1288 1304 1731 1704 1773 1580 1385 1517 1492 1538 1700 2180 1356 1306 811 790 2261 1347 1243 g 1198 1386 792 1050 2510 1465 1256 1293 1570 1491 1711 1728 1563 1566 1465 1405 1582 1720 1709 1692 1516 861 1393 1425 2218 2304 797 1289 1439 t 452 434 195 401 178 105 406 569 161 114 109 124 126 149 137 143 130 125 154 161 171 253 384 368 237 209 226 448 440

oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4) 0.773 0.644 1.421 0.545 0.952 1.875 0.953 24 5 20 10 10 23 15 15.286 15
; dyads_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=2/4; ncol2=24; w=20; offset=0; strand=D; shift=1; score=15.2857; -sssssscgCGCCCCGCCCvsssss---- ; cor=0.773; Ncor=0.644; logoDP=1.421; NIcor=0.545; NsEucl=0.952; SSD=1.875; NSW=0.953; rcor=24; rNcor=5; rlogoDP=20; rNIcor=10; rNsEucl=10; rSSD=23; rNSW=15; rank_mean=15.286; match_rank=15 a 0 153 137 120 109 106 88 107 81 62 81 55 67 55 60 59 61 55 35 327 68 105 94 162 157 0 0 0 0 c 0 514 510 621 396 680 723 734 305 887 202 918 840 880 853 158 886 882 934 392 311 313 340 535 476 0 0 0 0 g 0 386 435 329 600 332 316 276 744 207 850 190 239 239 218 941 226 244 200 376 776 732 699 373 418 0 0 0 0 t 0 171 142 154 119 106 97 107 94 68 91 61 78 50 93 66 51 43 55 129 69 74 91 154 173 0 0 0 0

oligos_7nt_test_vs_ctrl_m3_shift9 (oligos_7nt_test_vs_ctrl_m3) 0.798 0.456 1.269 0.435 0.930 1.419 0.941 19 23 23 20 28 16 25 22.000 24
; dyads_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=3/4; ncol2=13; w=12; offset=8; strand=D; shift=9; score= 22; ---------ssCcCCGCCCCss------- ; cor=0.798; Ncor=0.456; logoDP=1.269; NIcor=0.435; NsEucl=0.930; SSD=1.419; NSW=0.941; rcor=19; rNcor=23; rlogoDP=23; rNIcor=20; rNsEucl=28; rSSD=16; rNSW=25; rank_mean=22.000; match_rank=24 a 0 0 0 0 0 0 0 0 0 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m1_shift8 (oligos_6nt_test_vs_ctrl_m1) 0.761 0.430 1.116 0.389 0.931 1.613 0.938 27 26 26 24 26 20 26 25.000 28
; dyads_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=4/4; ncol2=16; w=13; offset=7; strand=D; shift=8; score= 25; --------sssgCCGCCCCGCCss----- ; cor=0.761; Ncor=0.430; logoDP=1.116; NIcor=0.389; NsEucl=0.931; SSD=1.613; NSW=0.938; rcor=27; rNcor=26; rlogoDP=26; rNIcor=24; rNsEucl=26; rSSD=20; rNSW=26; rank_mean=25.000; match_rank=28 a 0 0 0 0 0 0 0 0 178 210 115 69 64 74 71 36 50 53 76 63 80 71 162 161 0 0 0 0 0 c 0 0 0 0 0 0 0 0 601 517 356 308 1049 1061 98 1167 1019 1009 1028 156 951 976 568 541 0 0 0 0 0 g 0 0 0 0 0 0 0 0 423 471 827 929 201 178 1129 131 253 246 187 1082 266 251 448 481 0 0 0 0 0 t 0 0 0 0 0 0 0 0 176 180 80 72 64 65 80 44 56 70 87 77 81 80 200 195 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_m4_shift1 (dyads_test_vs_ctrl_m4)																	; dyads_test_vs_ctrl_m4; m=0 (reference); ncol1=20; shift=1; ncol=29; -ssGGCssssssssssCCCss-------- ; Alignment reference a 0 380 415 136 98 92 249 206 50 520 359 261 57 59 391 91 143 143 134 366 335 0 0 0 0 0 0 0 0 c 0 1221 1138 533 373 2485 1396 1251 1519 1054 1112 1102 1381 1463 1386 1250 2007 2001 2038 1031 971 0 0 0 0 0 0 0 0 g 0 939 962 2082 2291 229 927 961 1233 1255 1368 1473 1198 1030 1031 1440 584 582 543 1039 1212 0 0 0 0 0 0 0 0 t 0 345 370 134 123 79 313 467 83 56 46 49 249 333 77 104 151 159 170 449 367 0 0 0 0 0 0 0 0
dyads_test_vs_ctrl_m5_shift0 (dyads_test_vs_ctrl_m5)	0.826	0.570	1.146	0.480	0.961	1.210	0.970	12	12	25	16	1	8	5	11.286	10	; dyads_test_vs_ctrl_m4 versus dyads_test_vs_ctrl_m5; m=1/4; ncol2=29; w=20; offset=-1; strand=D; shift=0; score=11.2857; sscvGsssssssssssssssscssggcss ; cor=0.826; Ncor=0.570; logoDP=1.146; NIcor=0.480; NsEucl=0.961; SSD=1.210; NSW=0.970; rcor=12; rNcor=12; rlogoDP=25; rNIcor=16; rNsEucl=1; rSSD=8; rNSW=5; rank_mean=11.286; match_rank=10 a 425 389 218 1033 168 134 106 112 128 555 439 391 127 128 172 419 450 185 192 156 160 253 414 448 281 244 263 463 425 c 1472 1338 2342 1063 691 1843 1779 1573 1688 1387 1288 1304 1731 1704 1773 1580 1385 1517 1492 1538 1700 2180 1356 1306 811 790 2261 1347 1243 g 1198 1386 792 1050 2510 1465 1256 1293 1570 1491 1711 1728 1563 1566 1465 1405 1582 1720 1709 1692 1516 861 1393 1425 2218 2304 797 1289 1439 t 452 434 195 401 178 105 406 569 161 114 109 124 126 149 137 143 130 125 154 161 171 253 384 368 237 209 226 448 440
oligos_6nt_test_vs_ctrl_m4_shift1 (oligos_6nt_test_vs_ctrl_m4)	0.773	0.644	1.421	0.545	0.952	1.875	0.953	24	5	20	10	10	23	15	15.286	15	; dyads_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=2/4; ncol2=24; w=20; offset=0; strand=D; shift=1; score=15.2857; -sssssscgCGCCCCGCCCvsssss---- ; cor=0.773; Ncor=0.644; logoDP=1.421; NIcor=0.545; NsEucl=0.952; SSD=1.875; NSW=0.953; rcor=24; rNcor=5; rlogoDP=20; rNIcor=10; rNsEucl=10; rSSD=23; rNSW=15; rank_mean=15.286; match_rank=15 a 0 153 137 120 109 106 88 107 81 62 81 55 67 55 60 59 61 55 35 327 68 105 94 162 157 0 0 0 0 c 0 514 510 621 396 680 723 734 305 887 202 918 840 880 853 158 886 882 934 392 311 313 340 535 476 0 0 0 0 g 0 386 435 329 600 332 316 276 744 207 850 190 239 239 218 941 226 244 200 376 776 732 699 373 418 0 0 0 0 t 0 171 142 154 119 106 97 107 94 68 91 61 78 50 93 66 51 43 55 129 69 74 91 154 173 0 0 0 0
oligos_7nt_test_vs_ctrl_m3_shift9 (oligos_7nt_test_vs_ctrl_m3)	0.798	0.456	1.269	0.435	0.930	1.419	0.941	19	23	23	20	28	16	25	22.000	24	; dyads_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m3; m=3/4; ncol2=13; w=12; offset=8; strand=D; shift=9; score= 22; ---------ssCcCCGCCCCss------- ; cor=0.798; Ncor=0.456; logoDP=1.269; NIcor=0.435; NsEucl=0.930; SSD=1.419; NSW=0.941; rcor=19; rNcor=23; rlogoDP=23; rNIcor=20; rNsEucl=28; rSSD=16; rNSW=25; rank_mean=22.000; match_rank=24 a 0 0 0 0 0 0 0 0 0 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m1_shift8 (oligos_6nt_test_vs_ctrl_m1)	0.761	0.430	1.116	0.389	0.931	1.613	0.938	27	26	26	24	26	20	26	25.000	28	; dyads_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=4/4; ncol2=16; w=13; offset=7; strand=D; shift=8; score= 25; --------sssgCCGCCCCGCCss----- ; cor=0.761; Ncor=0.430; logoDP=1.116; NIcor=0.389; NsEucl=0.931; SSD=1.613; NSW=0.938; rcor=27; rNcor=26; rlogoDP=26; rNIcor=24; rNsEucl=26; rSSD=20; rNSW=26; rank_mean=25.000; match_rank=28 a 0 0 0 0 0 0 0 0 178 210 115 69 64 74 71 36 50 53 76 63 80 71 162 161 0 0 0 0 0 c 0 0 0 0 0 0 0 0 601 517 356 308 1049 1061 98 1167 1019 1009 1028 156 951 976 568 541 0 0 0 0 0 g 0 0 0 0 0 0 0 0 423 471 827 929 201 178 1129 131 253 246 187 1082 266 251 448 481 0 0 0 0 0 t 0 0 0 0 0 0 0 0 176 180 80 72 64 65 80 44 56 70 87 77 81 80 200 195 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_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
dyads_test_vs_ctrl_m1_shift0 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=0; ncol=29; 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 0 0 0 0 0 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 0 0 0 0 0 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 0 0 0 0 0 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 0 0 0 0 0

oligos_7nt_test_vs_ctrl_m1_rc_shift2 (oligos_7nt_test_vs_ctrl_m1_rc) 0.850 0.496 3.212 0.419 0.942 1.322 0.953 9 18 2 21 18 12 16 13.714 13
; dyads_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1_rc; m=1/2; ncol2=14; w=14; offset=2; strand=R; shift=2; score=13.7143; --ssgcCCtGGGGCsg------------- ; cor=0.850; Ncor=0.496; logoDP=3.212; NIcor=0.419; NsEucl=0.942; SSD=1.322; NSW=0.953; rcor=9; rNcor=18; rlogoDP=2; rNIcor=21; rNsEucl=18; rSSD=12; rNSW=16; rank_mean=13.714; match_rank=13 a 0 0 235 202 101 114 15 10 32 16 36 27 32 72 242 210 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 448 425 185 747 1134 1147 248 132 117 138 58 1071 350 314 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 410 359 849 283 101 89 179 1108 1093 1083 1140 70 431 548 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 174 281 132 123 17 21 808 11 21 19 37 54 244 195 0 0 0 0 0 0 0 0 0 0 0 0 0

dyads_test_vs_ctrl_m4_shift9 (dyads_test_vs_ctrl_m4) 0.787 0.407 1.506 0.391 0.944 1.429 0.952 22 28 19 23 17 17 18 20.571 21
; dyads_test_vs_ctrl_m1 versus dyads_test_vs_ctrl_m4; m=2/2; ncol2=20; w=15; offset=9; strand=D; shift=9; score=20.5714; ---------ssGGCssssssssssCCCss ; cor=0.787; Ncor=0.407; logoDP=1.506; NIcor=0.391; NsEucl=0.944; SSD=1.429; NSW=0.952; rcor=22; rNcor=28; rlogoDP=19; rNIcor=23; rNsEucl=17; rSSD=17; rNSW=18; rank_mean=20.571; match_rank=21 a 0 0 0 0 0 0 0 0 0 380 415 136 98 92 249 206 50 520 359 261 57 59 391 91 143 143 134 366 335 c 0 0 0 0 0 0 0 0 0 1221 1138 533 373 2485 1396 1251 1519 1054 1112 1102 1381 1463 1386 1250 2007 2001 2038 1031 971 g 0 0 0 0 0 0 0 0 0 939 962 2082 2291 229 927 961 1233 1255 1368 1473 1198 1030 1031 1440 584 582 543 1039 1212 t 0 0 0 0 0 0 0 0 0 345 370 134 123 79 313 467 83 56 46 49 249 333 77 104 151 159 170 449 367

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=29; 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 0 0 0 0 0 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 0 0 0 0 0 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 0 0 0 0 0 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 0 0 0 0 0
oligos_7nt_test_vs_ctrl_m1_rc_shift2 (oligos_7nt_test_vs_ctrl_m1_rc)	0.850	0.496	3.212	0.419	0.942	1.322	0.953	9	18	2	21	18	12	16	13.714	13	; dyads_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1_rc; m=1/2; ncol2=14; w=14; offset=2; strand=R; shift=2; score=13.7143; --ssgcCCtGGGGCsg------------- ; cor=0.850; Ncor=0.496; logoDP=3.212; NIcor=0.419; NsEucl=0.942; SSD=1.322; NSW=0.953; rcor=9; rNcor=18; rlogoDP=2; rNIcor=21; rNsEucl=18; rSSD=12; rNSW=16; rank_mean=13.714; match_rank=13 a 0 0 235 202 101 114 15 10 32 16 36 27 32 72 242 210 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 448 425 185 747 1134 1147 248 132 117 138 58 1071 350 314 0 0 0 0 0 0 0 0 0 0 0 0 0 g 0 0 410 359 849 283 101 89 179 1108 1093 1083 1140 70 431 548 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 174 281 132 123 17 21 808 11 21 19 37 54 244 195 0 0 0 0 0 0 0 0 0 0 0 0 0
dyads_test_vs_ctrl_m4_shift9 (dyads_test_vs_ctrl_m4)	0.787	0.407	1.506	0.391	0.944	1.429	0.952	22	28	19	23	17	17	18	20.571	21	; dyads_test_vs_ctrl_m1 versus dyads_test_vs_ctrl_m4; m=2/2; ncol2=20; w=15; offset=9; strand=D; shift=9; score=20.5714; ---------ssGGCssssssssssCCCss ; cor=0.787; Ncor=0.407; logoDP=1.506; NIcor=0.391; NsEucl=0.944; SSD=1.429; NSW=0.952; rcor=22; rNcor=28; rlogoDP=19; rNIcor=23; rNsEucl=17; rSSD=17; rNSW=18; rank_mean=20.571; match_rank=21 a 0 0 0 0 0 0 0 0 0 380 415 136 98 92 249 206 50 520 359 261 57 59 391 91 143 143 134 366 335 c 0 0 0 0 0 0 0 0 0 1221 1138 533 373 2485 1396 1251 1519 1054 1112 1102 1381 1463 1386 1250 2007 2001 2038 1031 971 g 0 0 0 0 0 0 0 0 0 939 962 2082 2291 229 927 961 1233 1255 1368 1473 1198 1030 1031 1440 584 582 543 1039 1212 t 0 0 0 0 0 0 0 0 0 345 370 134 123 79 313 467 83 56 46 49 249 333 77 104 151 159 170 449 367

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m3_shift9 ; 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_test_vs_ctrl_m3_shift9 (dyads_test_vs_ctrl_m3)
; dyads_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=9; ncol=24; ---------ssGCCbsvsGCCtss ; Alignment reference a 0 0 0 0 0 0 0 0 0 159 182 24 26 22 9 102 311 14 30 18 36 92 122 179 c 0 0 0 0 0 0 0 0 0 456 389 50 1006 972 486 521 367 395 48 1028 924 202 428 334 g 0 0 0 0 0 0 0 0 0 337 330 1014 67 101 308 384 431 700 1010 56 125 258 392 410 t 0 0 0 0 0 0 0 0 0 166 217 30 19 23 315 111 9 9 30 16 33 566 176 195

oligos_7nt_test_vs_ctrl_m1_shift9 (oligos_7nt_test_vs_ctrl_m1) 0.779 0.727 3.541 0.684 0.931 1.879 0.933 23 2 1 3 27 24 28 15.429 16
; dyads_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=1/3; ncol2=14; w=14; offset=0; strand=D; shift=9; score=15.4286; ---------csGCCCCaGGgcss- ; cor=0.779; Ncor=0.727; logoDP=3.541; NIcor=0.684; NsEucl=0.931; SSD=1.879; NSW=0.933; rcor=23; rNcor=2; rlogoDP=1; rNIcor=3; rNsEucl=27; rSSD=24; rNSW=28; rank_mean=15.429; match_rank=16 a 0 0 0 0 0 0 0 0 0 195 244 54 37 19 21 11 808 21 17 123 132 281 174 0 c 0 0 0 0 0 0 0 0 0 548 431 70 1140 1083 1093 1108 179 89 101 283 849 359 410 0 g 0 0 0 0 0 0 0 0 0 314 350 1071 58 138 117 132 248 1147 1134 747 185 425 448 0 t 0 0 0 0 0 0 0 0 0 210 242 72 32 27 36 16 32 10 15 114 101 202 235 0

dyads_test_vs_ctrl_m4_rc_shift3 (dyads_test_vs_ctrl_m4_rc) 0.821 0.547 1.293 0.317 0.942 1.322 0.953 13 15 21 26 19 13 17 17.714 18
; dyads_test_vs_ctrl_m3 versus dyads_test_vs_ctrl_m4_rc; m=2/3; ncol2=20; w=14; offset=-6; strand=R; shift=3; score=17.7143; ---ssGGGssssssssssGCCss- ; cor=0.821; Ncor=0.547; logoDP=1.293; NIcor=0.317; NsEucl=0.942; SSD=1.322; NSW=0.953; rcor=13; rNcor=15; rlogoDP=21; rNIcor=26; rNsEucl=19; rSSD=13; rNSW=17; rank_mean=17.714; match_rank=18 a 0 0 0 367 449 170 159 151 104 77 333 249 49 46 56 83 467 313 79 123 134 370 345 0 c 0 0 0 1212 1039 543 582 584 1440 1031 1030 1198 1473 1368 1255 1233 961 927 229 2291 2082 962 939 0 g 0 0 0 971 1031 2038 2001 2007 1250 1386 1463 1381 1102 1112 1054 1519 1251 1396 2485 373 533 1138 1221 0 t 0 0 0 335 366 134 143 143 91 391 59 57 261 359 520 50 206 249 92 98 136 415 380 0

oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5) 0.759 0.474 2.337 0.437 0.935 1.904 0.937 28 21 11 19 24 25 27 22.143 25
; dyads_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5; m=3/3; ncol2=24; w=15; offset=-9; strand=D; shift=0; score=22.1429; sssccvGCCCCGCCCCvGggCsss ; cor=0.759; Ncor=0.474; logoDP=2.337; NIcor=0.437; NsEucl=0.935; SSD=1.904; NSW=0.937; rcor=28; rNcor=21; rlogoDP=11; rNIcor=19; rNsEucl=24; rSSD=25; rNSW=27; rank_mean=22.143; match_rank=25 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

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_m3_shift9 (dyads_test_vs_ctrl_m3)																	; dyads_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=9; ncol=24; ---------ssGCCbsvsGCCtss ; Alignment reference a 0 0 0 0 0 0 0 0 0 159 182 24 26 22 9 102 311 14 30 18 36 92 122 179 c 0 0 0 0 0 0 0 0 0 456 389 50 1006 972 486 521 367 395 48 1028 924 202 428 334 g 0 0 0 0 0 0 0 0 0 337 330 1014 67 101 308 384 431 700 1010 56 125 258 392 410 t 0 0 0 0 0 0 0 0 0 166 217 30 19 23 315 111 9 9 30 16 33 566 176 195
oligos_7nt_test_vs_ctrl_m1_shift9 (oligos_7nt_test_vs_ctrl_m1)	0.779	0.727	3.541	0.684	0.931	1.879	0.933	23	2	1	3	27	24	28	15.429	16	; dyads_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m1; m=1/3; ncol2=14; w=14; offset=0; strand=D; shift=9; score=15.4286; ---------csGCCCCaGGgcss- ; cor=0.779; Ncor=0.727; logoDP=3.541; NIcor=0.684; NsEucl=0.931; SSD=1.879; NSW=0.933; rcor=23; rNcor=2; rlogoDP=1; rNIcor=3; rNsEucl=27; rSSD=24; rNSW=28; rank_mean=15.429; match_rank=16 a 0 0 0 0 0 0 0 0 0 195 244 54 37 19 21 11 808 21 17 123 132 281 174 0 c 0 0 0 0 0 0 0 0 0 548 431 70 1140 1083 1093 1108 179 89 101 283 849 359 410 0 g 0 0 0 0 0 0 0 0 0 314 350 1071 58 138 117 132 248 1147 1134 747 185 425 448 0 t 0 0 0 0 0 0 0 0 0 210 242 72 32 27 36 16 32 10 15 114 101 202 235 0
dyads_test_vs_ctrl_m4_rc_shift3 (dyads_test_vs_ctrl_m4_rc)	0.821	0.547	1.293	0.317	0.942	1.322	0.953	13	15	21	26	19	13	17	17.714	18	; dyads_test_vs_ctrl_m3 versus dyads_test_vs_ctrl_m4_rc; m=2/3; ncol2=20; w=14; offset=-6; strand=R; shift=3; score=17.7143; ---ssGGGssssssssssGCCss- ; cor=0.821; Ncor=0.547; logoDP=1.293; NIcor=0.317; NsEucl=0.942; SSD=1.322; NSW=0.953; rcor=13; rNcor=15; rlogoDP=21; rNIcor=26; rNsEucl=19; rSSD=13; rNSW=17; rank_mean=17.714; match_rank=18 a 0 0 0 367 449 170 159 151 104 77 333 249 49 46 56 83 467 313 79 123 134 370 345 0 c 0 0 0 1212 1039 543 582 584 1440 1031 1030 1198 1473 1368 1255 1233 961 927 229 2291 2082 962 939 0 g 0 0 0 971 1031 2038 2001 2007 1250 1386 1463 1381 1102 1112 1054 1519 1251 1396 2485 373 533 1138 1221 0 t 0 0 0 335 366 134 143 143 91 391 59 57 261 359 520 50 206 249 92 98 136 415 380 0
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5)	0.759	0.474	2.337	0.437	0.935	1.904	0.937	28	21	11	19	24	25	27	22.143	25	; dyads_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5; m=3/3; ncol2=24; w=15; offset=-9; strand=D; shift=0; score=22.1429; sssccvGCCCCGCCCCvGggCsss ; cor=0.759; Ncor=0.474; logoDP=2.337; NIcor=0.437; NsEucl=0.935; SSD=1.904; NSW=0.937; rcor=28; rNcor=21; rlogoDP=11; rNIcor=19; rNsEucl=24; rSSD=25; rNSW=27; rank_mean=22.143; match_rank=25 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

One-to-n matrix alignment; reference matrix: dyads_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
dyads_test_vs_ctrl_m5_shift0 (dyads_test_vs_ctrl_m5)
; dyads_test_vs_ctrl_m5; m=0 (reference); ncol1=29; shift=0; ncol=33; sscvGsssssssssssssssscssggcss---- ; Alignment reference a 425 389 218 1033 168 134 106 112 128 555 439 391 127 128 172 419 450 185 192 156 160 253 414 448 281 244 263 463 425 0 0 0 0 c 1472 1338 2342 1063 691 1843 1779 1573 1688 1387 1288 1304 1731 1704 1773 1580 1385 1517 1492 1538 1700 2180 1356 1306 811 790 2261 1347 1243 0 0 0 0 g 1198 1386 792 1050 2510 1465 1256 1293 1570 1491 1711 1728 1563 1566 1465 1405 1582 1720 1709 1692 1516 861 1393 1425 2218 2304 797 1289 1439 0 0 0 0 t 452 434 195 401 178 105 406 569 161 114 109 124 126 149 137 143 130 125 154 161 171 253 384 368 237 209 226 448 440 0 0 0 0

oligos_6nt_test_vs_ctrl_m4_shift4 (oligos_6nt_test_vs_ctrl_m4) 0.765 0.633 1.286 0.524 0.957 2.095 0.956 25 7 22 12 5 29 11 15.857 17
; dyads_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4; m=1/2; ncol2=24; w=24; offset=4; strand=D; shift=4; score=15.8571; ----sssssscgCGCCCCGCCCvsssss----- ; cor=0.765; Ncor=0.633; logoDP=1.286; NIcor=0.524; NsEucl=0.957; SSD=2.095; NSW=0.956; rcor=25; rNcor=7; rlogoDP=22; rNIcor=12; rNsEucl=5; rSSD=29; rNSW=11; rank_mean=15.857; match_rank=17 a 0 0 0 0 153 137 120 109 106 88 107 81 62 81 55 67 55 60 59 61 55 35 327 68 105 94 162 157 0 0 0 0 0 c 0 0 0 0 514 510 621 396 680 723 734 305 887 202 918 840 880 853 158 886 882 934 392 311 313 340 535 476 0 0 0 0 0 g 0 0 0 0 386 435 329 600 332 316 276 744 207 850 190 239 239 218 941 226 244 200 376 776 732 699 373 418 0 0 0 0 0 t 0 0 0 0 171 142 154 119 106 97 107 94 68 91 61 78 50 93 66 51 43 55 129 69 74 91 154 173 0 0 0 0 0

oligos_6nt_test_vs_ctrl_m5_rc_shift9 (oligos_6nt_test_vs_ctrl_m5_rc) 0.763 0.463 1.005 0.225 0.949 2.086 0.948 26 22 27 27 14 28 20 23.429 27
; dyads_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5_rc; m=2/2; ncol2=24; w=20; offset=9; strand=R; shift=9; score=23.4286; ---------sssGccCbGGGGCGGGGCbggsss ; cor=0.763; Ncor=0.463; logoDP=1.005; NIcor=0.225; NsEucl=0.949; SSD=2.086; NSW=0.948; rcor=26; rNcor=22; rlogoDP=27; rNIcor=27; rNsEucl=14; rSSD=28; rNSW=20; rank_mean=23.429; match_rank=27 a 0 0 0 0 0 0 0 0 0 88 82 89 35 36 29 26 58 27 46 30 27 42 59 43 40 26 46 73 30 46 66 107 98 c 0 0 0 0 0 0 0 0 0 214 236 203 71 421 429 482 187 106 91 97 103 528 82 94 110 84 461 177 119 135 376 204 195 g 0 0 0 0 0 0 0 0 0 255 261 218 514 147 146 110 168 485 494 506 489 43 472 487 457 499 107 198 440 424 165 251 259 t 0 0 0 0 0 0 0 0 0 96 74 143 33 49 49 35 240 35 22 20 34 40 40 29 46 44 39 205 64 48 46 91 101

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_m5_shift0 (dyads_test_vs_ctrl_m5)																	; dyads_test_vs_ctrl_m5; m=0 (reference); ncol1=29; shift=0; ncol=33; sscvGsssssssssssssssscssggcss---- ; Alignment reference a 425 389 218 1033 168 134 106 112 128 555 439 391 127 128 172 419 450 185 192 156 160 253 414 448 281 244 263 463 425 0 0 0 0 c 1472 1338 2342 1063 691 1843 1779 1573 1688 1387 1288 1304 1731 1704 1773 1580 1385 1517 1492 1538 1700 2180 1356 1306 811 790 2261 1347 1243 0 0 0 0 g 1198 1386 792 1050 2510 1465 1256 1293 1570 1491 1711 1728 1563 1566 1465 1405 1582 1720 1709 1692 1516 861 1393 1425 2218 2304 797 1289 1439 0 0 0 0 t 452 434 195 401 178 105 406 569 161 114 109 124 126 149 137 143 130 125 154 161 171 253 384 368 237 209 226 448 440 0 0 0 0
oligos_6nt_test_vs_ctrl_m4_shift4 (oligos_6nt_test_vs_ctrl_m4)	0.765	0.633	1.286	0.524	0.957	2.095	0.956	25	7	22	12	5	29	11	15.857	17	; dyads_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m4; m=1/2; ncol2=24; w=24; offset=4; strand=D; shift=4; score=15.8571; ----sssssscgCGCCCCGCCCvsssss----- ; cor=0.765; Ncor=0.633; logoDP=1.286; NIcor=0.524; NsEucl=0.957; SSD=2.095; NSW=0.956; rcor=25; rNcor=7; rlogoDP=22; rNIcor=12; rNsEucl=5; rSSD=29; rNSW=11; rank_mean=15.857; match_rank=17 a 0 0 0 0 153 137 120 109 106 88 107 81 62 81 55 67 55 60 59 61 55 35 327 68 105 94 162 157 0 0 0 0 0 c 0 0 0 0 514 510 621 396 680 723 734 305 887 202 918 840 880 853 158 886 882 934 392 311 313 340 535 476 0 0 0 0 0 g 0 0 0 0 386 435 329 600 332 316 276 744 207 850 190 239 239 218 941 226 244 200 376 776 732 699 373 418 0 0 0 0 0 t 0 0 0 0 171 142 154 119 106 97 107 94 68 91 61 78 50 93 66 51 43 55 129 69 74 91 154 173 0 0 0 0 0
oligos_6nt_test_vs_ctrl_m5_rc_shift9 (oligos_6nt_test_vs_ctrl_m5_rc)	0.763	0.463	1.005	0.225	0.949	2.086	0.948	26	22	27	27	14	28	20	23.429	27	; dyads_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5_rc; m=2/2; ncol2=24; w=20; offset=9; strand=R; shift=9; score=23.4286; ---------sssGccCbGGGGCGGGGCbggsss ; cor=0.763; Ncor=0.463; logoDP=1.005; NIcor=0.225; NsEucl=0.949; SSD=2.086; NSW=0.948; rcor=26; rNcor=22; rlogoDP=27; rNIcor=27; rNsEucl=14; rSSD=28; rNSW=20; rank_mean=23.429; match_rank=27 a 0 0 0 0 0 0 0 0 0 88 82 89 35 36 29 26 58 27 46 30 27 42 59 43 40 26 46 73 30 46 66 107 98 c 0 0 0 0 0 0 0 0 0 214 236 203 71 421 429 482 187 106 91 97 103 528 82 94 110 84 461 177 119 135 376 204 195 g 0 0 0 0 0 0 0 0 0 255 261 218 514 147 146 110 168 485 494 506 489 43 472 487 457 499 107 198 440 424 165 251 259 t 0 0 0 0 0 0 0 0 0 96 74 143 33 49 49 35 240 35 22 20 34 40 40 29 46 44 39 205 64 48 46 91 101

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift4 ; 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_7nt_test_vs_ctrl_m1_shift4 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=14; shift=4; ncol=18; ----csGCCCCaGGgcss ; Alignment reference a 0 0 0 0 195 244 54 37 19 21 11 808 21 17 123 132 281 174 c 0 0 0 0 548 431 70 1140 1083 1093 1108 179 89 101 283 849 359 410 g 0 0 0 0 314 350 1071 58 138 117 132 248 1147 1134 747 185 425 448 t 0 0 0 0 210 242 72 32 27 36 16 32 10 15 114 101 202 235

oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3) 0.804 0.402 2.545 0.380 0.910 1.310 0.927 18 29 6 25 29 11 29 21.000 22
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m3; m=1/1; ncol2=13; w=9; offset=-4; strand=D; shift=0; score= 21; ssCcCCGCCCCss----- ; cor=0.804; Ncor=0.402; logoDP=2.545; NIcor=0.380; NsEucl=0.910; SSD=1.310; NSW=0.927; rcor=18; rNcor=29; rlogoDP=6; rNIcor=25; rNsEucl=29; rSSD=11; rNSW=29; rank_mean=21.000; match_rank=22 a 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 0 0 c 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 0 0 g 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 0 0 t 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0 0 0