One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.211230_2025-05-26.211230_ZHQlvw/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/05/26/peak-motifs.2025-05-26.211230_2025-05-26.211230_ZHQlvw/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; mwTAGATAAwt ; Alignment reference a 158 137 6 320 30 340 0 337 319 99 80 c 95 41 5 0 11 8 5 0 7 39 32 g 54 27 2 1 246 1 1 1 5 53 53 t 44 146 338 30 64 2 345 13 20 160 186

oligos_7nt_mkv4_m4_shift0 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; mwTAGATAAwt ; cor=; Ncor= a 158 137 6 320 30 340 0 337 319 99 80 c 95 41 5 0 11 8 5 0 7 39 32 g 54 27 2 1 246 1 1 1 5 53 53 t 44 146 338 30 64 2 345 13 20 160 186

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=16; shift=0; ncol=16; aaaGAGCAAcAAAAAG ; Alignment reference a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; aaaGAGCAAcAAAAAG ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m2; m=2/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.920964; -aarAGCAACAAAAag ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m2; m=3/8; ncol2=14; w=0; offset=2; strand=D; shift=2; score=0.869473; --arAGCAACAAAAaG ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36

positions_7nt_m2_shift5 (positions_7nt_m2)
; oligos_6nt_mkv3_m4 versus positions_7nt_m2; m=4/8; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.629085; -----rcAACAAAAar ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55

positions_6nt_m2_shift4 (positions_6nt_m2)
; oligos_6nt_mkv3_m4 versus positions_6nt_m2; m=5/8; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.628839; ----agcAACAAAaa- ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 0 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 0 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 0 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72 0

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m3; m=6/8; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.499378; ----armAAGAAAra- ; cor=; Ncor= a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 0 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 0 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 0 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111 0

positions_7nt_m1_shift8 (positions_7nt_m1)
; oligos_6nt_mkv3_m4 versus positions_7nt_m1; m=7/8; ncol2=11; w=0; offset=8; strand=D; shift=8; score=0.405195; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0

positions_6nt_m1_shift8 (positions_6nt_m1)
; oligos_6nt_mkv3_m4 versus positions_6nt_m1; m=8/8; ncol2=11; w=0; offset=8; strand=D; shift=8; score=0.404758; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=14; shift=2; ncol=16; --arAGCAACAAAAaG ; Alignment reference a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=2; score= 1; --arAGCAACAAAAaG ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m2; m=2/8; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.927077; -aarAGCAACAAAAag ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m4; m=3/8; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.869473; aaaGAGCAAcAAAAAG ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32

positions_7nt_m2_shift5 (positions_7nt_m2)
; oligos_7nt_mkv4_m2 versus positions_7nt_m2; m=4/8; ncol2=11; w=0; offset=3; strand=D; shift=5; score=0.729885; -----rcAACAAAAar ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55

positions_6nt_m2_shift4 (positions_6nt_m2)
; oligos_7nt_mkv4_m2 versus positions_6nt_m2; m=5/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.724624; ----agcAACAAAaa- ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 0 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 0 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 0 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72 0

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m3; m=6/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.566341; ----armAAGAAAra- ; cor=; Ncor= a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 0 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 0 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 0 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111 0

positions_7nt_m1_shift8 (positions_7nt_m1)
; oligos_7nt_mkv4_m2 versus positions_7nt_m1; m=7/8; ncol2=11; w=0; offset=6; strand=D; shift=8; score=0.443444; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0

positions_6nt_m1_shift8 (positions_6nt_m1)
; oligos_7nt_mkv4_m2 versus positions_6nt_m1; m=8/8; ncol2=11; w=0; offset=6; strand=D; shift=8; score=0.44284; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; syCTCAGCCtc ; Alignment reference a 78 82 45 9 35 336 9 26 16 94 90 c 115 102 339 21 362 26 0 363 320 51 147 g 168 93 7 4 3 20 377 4 13 41 67 t 41 125 11 368 2 20 16 9 53 216 98

oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; syCTCAGCCtc ; cor=; Ncor= a 78 82 45 9 35 336 9 26 16 94 90 c 115 102 339 21 362 26 0 363 320 51 147 g 168 93 7 4 3 20 377 4 13 41 67 t 41 125 11 368 2 20 16 9 53 216 98

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift1 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=15; shift=1; ncol=16; -aarAGCAACAAAAag ; Alignment reference a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -aarAGCAACAAAAag ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m2; m=2/8; ncol2=14; w=0; offset=1; strand=D; shift=2; score=0.927077; --arAGCAACAAAAaG ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m4; m=3/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.920964; aaaGAGCAAcAAAAAG ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32

positions_7nt_m2_shift5 (positions_7nt_m2)
; oligos_6nt_mkv3_m2 versus positions_7nt_m2; m=4/8; ncol2=11; w=0; offset=4; strand=D; shift=5; score=0.68614; -----rcAACAAAAar ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55

positions_6nt_m2_shift4 (positions_6nt_m2)
; oligos_6nt_mkv3_m2 versus positions_6nt_m2; m=5/8; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.672963; ----agcAACAAAaa- ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 0 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 0 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 0 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72 0

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m3; m=6/8; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.523115; ----armAAGAAAra- ; cor=; Ncor= a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 0 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 0 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 0 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111 0

positions_7nt_m1_shift8 (positions_7nt_m1)
; oligos_6nt_mkv3_m2 versus positions_7nt_m1; m=7/8; ncol2=11; w=0; offset=7; strand=D; shift=8; score=0.418459; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0

positions_6nt_m1_shift8 (positions_6nt_m1)
; oligos_6nt_mkv3_m2 versus positions_6nt_m1; m=8/8; ncol2=11; w=0; offset=7; strand=D; shift=8; score=0.417936; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift4 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift4 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=11; shift=4; ncol=15; ----agcAACAAAaa ; Alignment reference a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72

positions_6nt_m2_shift4 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----agcAACAAAaa ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72

positions_7nt_m2_shift5 (positions_7nt_m2)
; positions_6nt_m2 versus positions_7nt_m2; m=2/8; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.803346; -----rcAACAAAAa ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; positions_6nt_m2 versus oligos_6nt_mkv3_m3; m=3/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.759816; ----armAAGAAAra ; cor=; Ncor= a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; positions_6nt_m2 versus oligos_7nt_mkv4_m2; m=4/8; ncol2=14; w=-2; offset=-2; strand=D; shift=2; score=0.724624; --arAGCAACAAAAa ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; positions_6nt_m2 versus oligos_6nt_mkv3_m2; m=5/8; ncol2=15; w=-3; offset=-3; strand=D; shift=1; score=0.672963; -aarAGCAACAAAAa ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; positions_6nt_m2 versus oligos_6nt_mkv3_m4; m=6/8; ncol2=16; w=-4; offset=-4; strand=D; shift=0; score=0.628839; aaaGAGCAAcAAAAA ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56

positions_7nt_m1_shift8 (positions_7nt_m1)
; positions_6nt_m2 versus positions_7nt_m1; m=7/8; ncol2=11; w=0; offset=4; strand=D; shift=8; score=0.407036; --------AyAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0

positions_6nt_m1_shift8 (positions_6nt_m1)
; positions_6nt_m2 versus positions_6nt_m1; m=8/8; ncol2=11; w=0; offset=4; strand=D; shift=8; score=0.406185; --------AyAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=13; shift=3; ncol=16; ---acAAAAAGGCAaa ; Alignment reference a 0 0 0 348 129 525 504 526 518 470 44 28 96 448 250 179 c 0 0 0 69 176 0 12 0 10 13 4 4 394 17 57 121 g 0 0 0 91 118 2 16 6 1 45 482 498 11 4 129 123 t 0 0 0 24 109 5 0 0 3 4 2 2 31 63 96 109

oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---acAAAAAGGCAaa ; cor=; Ncor= a 0 0 0 348 129 525 504 526 518 470 44 28 96 448 250 179 c 0 0 0 69 176 0 12 0 10 13 4 4 394 17 57 121 g 0 0 0 91 118 2 16 6 1 45 482 498 11 4 129 123 t 0 0 0 24 109 5 0 0 3 4 2 2 31 63 96 109

oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=2/5; ncol2=12; w=0; offset=1; strand=D; shift=4; score=0.892921; ----yaAAAAGGcwdd ; cor=; Ncor= a 0 0 0 0 117 355 556 566 534 548 8 9 88 372 194 174 c 0 0 0 0 199 75 2 3 22 13 5 0 366 40 50 101 g 0 0 0 0 82 35 11 2 0 6 559 563 54 12 147 150 t 0 0 0 0 174 107 3 1 16 5 0 0 64 148 181 147

positions_7nt_m1_shift3 (positions_7nt_m1)
; oligos_7nt_mkv4_m1 versus positions_7nt_m1; m=3/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.821285; ---AyAAAAAGGma-- ; cor=; Ncor= a 0 0 0 367 97 518 499 506 511 502 0 1 164 282 0 0 c 0 0 0 65 205 0 5 1 0 16 10 0 213 78 0 0 g 0 0 0 75 76 0 0 2 0 1 509 518 57 33 0 0 t 0 0 0 12 141 1 15 10 8 0 0 0 85 126 0 0

positions_6nt_m1_shift3 (positions_6nt_m1)
; oligos_7nt_mkv4_m1 versus positions_6nt_m1; m=4/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.821267; ---AyAAAAAGGma-- ; cor=; Ncor= a 0 0 0 370 100 517 505 512 517 509 0 1 165 287 0 0 c 0 0 0 65 205 0 5 1 0 16 10 0 214 79 0 0 g 0 0 0 76 76 0 0 2 0 0 515 524 58 32 0 0 t 0 0 0 14 144 8 15 10 8 0 0 0 88 127 0 0

positions_7nt_m2_shift0 (positions_7nt_m2)
; oligos_7nt_mkv4_m1 versus positions_7nt_m2; m=5/5; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.428388; rcAACAAAAar----- ; cor=; Ncor= a 147 67 454 456 0 403 426 434 455 229 151 0 0 0 0 0 c 61 214 0 1 438 0 5 0 0 103 31 0 0 0 0 0 g 216 62 2 0 0 13 0 0 0 51 220 0 0 0 0 0 t 33 114 1 0 19 41 26 23 2 74 55 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -yaAAAAGGcwdd ; Alignment reference a 0 117 355 556 566 534 548 8 9 88 372 194 174 c 0 199 75 2 3 22 13 5 0 366 40 50 101 g 0 82 35 11 2 0 6 559 563 54 12 147 150 t 0 174 107 3 1 16 5 0 0 64 148 181 147

oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -yaAAAAGGcwdd ; cor=; Ncor= a 0 117 355 556 566 534 548 8 9 88 372 194 174 c 0 199 75 2 3 22 13 5 0 366 40 50 101 g 0 82 35 11 2 0 6 559 563 54 12 147 150 t 0 174 107 3 1 16 5 0 0 64 148 181 147

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=2/4; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.892921; acAAAAAGGCAaa ; cor=; Ncor= a 348 129 525 504 526 518 470 44 28 96 448 250 179 c 69 176 0 12 0 10 13 4 4 394 17 57 121 g 91 118 2 16 6 1 45 482 498 11 4 129 123 t 24 109 5 0 0 3 4 2 2 31 63 96 109

positions_6nt_m1_shift0 (positions_6nt_m1)
; oligos_6nt_mkv3_m1 versus positions_6nt_m1; m=3/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.747084; AyAAAAAGGma-- ; cor=; Ncor= a 370 100 517 505 512 517 509 0 1 165 287 0 0 c 65 205 0 5 1 0 16 10 0 214 79 0 0 g 76 76 0 0 2 0 0 515 524 58 32 0 0 t 14 144 8 15 10 8 0 0 0 88 127 0 0

positions_7nt_m1_shift0 (positions_7nt_m1)
; oligos_6nt_mkv3_m1 versus positions_7nt_m1; m=4/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.746037; AyAAAAAGGma-- ; cor=; Ncor= a 367 97 518 499 506 511 502 0 1 164 282 0 0 c 65 205 0 5 1 0 16 10 0 213 78 0 0 g 75 76 0 0 2 0 1 509 518 57 33 0 0 t 12 141 1 15 10 8 0 0 0 85 126 0 0

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift5 ; 11 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift5 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=11; shift=5; ncol=16; -----rcAACAAAAar ; Alignment reference a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55

positions_7nt_m2_shift5 (positions_7nt_m2)
; positions_7nt_m2 versus positions_7nt_m2; m=1/10; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----rcAACAAAAar ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55

positions_6nt_m2_shift4 (positions_6nt_m2)
; positions_7nt_m2 versus positions_6nt_m2; m=2/10; ncol2=11; w=-1; offset=-1; strand=D; shift=4; score=0.803346; ----agcAACAAAaa- ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 0 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 0 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 0 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72 0

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; positions_7nt_m2 versus oligos_7nt_mkv4_m2; m=3/10; ncol2=14; w=-3; offset=-3; strand=D; shift=2; score=0.729885; --arAGCAACAAAAaG ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; positions_7nt_m2 versus oligos_6nt_mkv3_m2; m=4/10; ncol2=15; w=-4; offset=-4; strand=D; shift=1; score=0.68614; -aarAGCAACAAAAag ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; positions_7nt_m2 versus oligos_6nt_mkv3_m4; m=5/10; ncol2=16; w=-5; offset=-5; strand=D; shift=0; score=0.629085; aaaGAGCAAcAAAAAG ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; positions_7nt_m2 versus oligos_6nt_mkv3_m3; m=6/10; ncol2=11; w=-1; offset=-1; strand=D; shift=4; score=0.619786; ----armAAGAAAra- ; cor=; Ncor= a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 0 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 0 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 0 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111 0

oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)
; positions_7nt_m2 versus oligos_7nt_mkv4_m3; m=7/10; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.587849; ------raACTAAAAy ; cor=; Ncor= a 0 0 0 0 0 0 77 117 228 24 0 207 166 187 224 50 c 0 0 0 0 0 0 35 28 0 201 1 0 25 1 0 67 g 0 0 0 0 0 0 79 32 0 1 3 18 6 5 3 42 t 0 0 0 0 0 0 37 51 0 2 224 3 31 35 1 69

positions_7nt_m1_shift8 (positions_7nt_m1)
; positions_7nt_m2 versus positions_7nt_m1; m=8/10; ncol2=11; w=0; offset=3; strand=D; shift=8; score=0.49067; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0

positions_6nt_m1_shift8 (positions_6nt_m1)
; positions_7nt_m2 versus positions_6nt_m1; m=9/10; ncol2=11; w=0; offset=3; strand=D; shift=8; score=0.489966; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0

oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)
; positions_7nt_m2 versus oligos_7nt_mkv4_m1; m=10/10; ncol2=13; w=0; offset=3; strand=D; shift=8; score=0.428388; --------acAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 348 129 525 504 526 518 470 44 c 0 0 0 0 0 0 0 0 69 176 0 12 0 10 13 4 g 0 0 0 0 0 0 0 0 91 118 2 16 6 1 45 482 t 0 0 0 0 0 0 0 0 24 109 5 0 0 3 4 2

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift4 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=4; ncol=15; ----armAAGAAAra ; Alignment reference a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111

oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----armAAGAAAra ; cor=; Ncor= a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111

positions_6nt_m2_shift4 (positions_6nt_m2)
; oligos_6nt_mkv3_m3 versus positions_6nt_m2; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.759816; ----agcAACAAAaa ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72

positions_7nt_m2_shift5 (positions_7nt_m2)
; oligos_6nt_mkv3_m3 versus positions_7nt_m2; m=3/6; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.619786; -----rcAACAAAAa ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2; m=4/6; ncol2=14; w=-2; offset=-2; strand=D; shift=2; score=0.566341; --arAGCAACAAAAa ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m2; m=5/6; ncol2=15; w=-3; offset=-3; strand=D; shift=1; score=0.523115; -aarAGCAACAAAAa ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m4; m=6/6; ncol2=16; w=-4; offset=-4; strand=D; shift=0; score=0.499378; aaaGAGCAAcAAAAA ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift8 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift8 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=11; shift=8; ncol=19; --------AyAAAAAGGma ; Alignment reference a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 1 165 287 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 0 214 79 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 524 58 32 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0 0 88 127

positions_6nt_m1_shift8 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/9; ncol2=11; w=0; offset=0; strand=D; shift=8; score= 1; --------AyAAAAAGGma ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 1 165 287 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 0 214 79 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 524 58 32 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0 0 88 127

positions_7nt_m1_shift8 (positions_7nt_m1)
; positions_6nt_m1 versus positions_7nt_m1; m=2/9; ncol2=11; w=0; offset=0; strand=D; shift=8; score=0.999959; --------AyAAAAAGGma ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 1 164 282 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 0 213 78 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 518 57 33 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0 0 85 126

oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)
; positions_6nt_m1 versus oligos_7nt_mkv4_m1; m=3/9; ncol2=13; w=0; offset=0; strand=D; shift=8; score=0.821267; --------acAAAAAGGCA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 348 129 525 504 526 518 470 44 28 96 448 c 0 0 0 0 0 0 0 0 69 176 0 12 0 10 13 4 4 394 17 g 0 0 0 0 0 0 0 0 91 118 2 16 6 1 45 482 498 11 4 t 0 0 0 0 0 0 0 0 24 109 5 0 0 3 4 2 2 31 63

oligos_6nt_mkv3_m1_shift9 (oligos_6nt_mkv3_m1)
; positions_6nt_m1 versus oligos_6nt_mkv3_m1; m=4/9; ncol2=12; w=0; offset=1; strand=D; shift=9; score=0.747084; ---------yaAAAAGGcw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 117 355 556 566 534 548 8 9 88 372 c 0 0 0 0 0 0 0 0 0 199 75 2 3 22 13 5 0 366 40 g 0 0 0 0 0 0 0 0 0 82 35 11 2 0 6 559 563 54 12 t 0 0 0 0 0 0 0 0 0 174 107 3 1 16 5 0 0 64 148

positions_7nt_m2_shift5 (positions_7nt_m2)
; positions_6nt_m1 versus positions_7nt_m2; m=5/9; ncol2=11; w=-3; offset=-3; strand=D; shift=5; score=0.489966; -----rcAACAAAAar--- ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 0 0 0 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 0 0 0 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 0 0 0 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55 0 0 0

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; positions_6nt_m1 versus oligos_7nt_mkv4_m2; m=6/9; ncol2=14; w=-6; offset=-6; strand=D; shift=2; score=0.44284; --arAGCAACAAAAaG--- ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 0 0 0 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 0 0 0 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 0 0 0 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36 0 0 0

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; positions_6nt_m1 versus oligos_6nt_mkv3_m2; m=7/9; ncol2=15; w=-7; offset=-7; strand=D; shift=1; score=0.417936; -aarAGCAACAAAAag--- ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 0 0 0 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 0 0 0 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 0 0 0 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41 0 0 0

positions_6nt_m2_shift4 (positions_6nt_m2)
; positions_6nt_m1 versus positions_6nt_m2; m=8/9; ncol2=11; w=-4; offset=-4; strand=D; shift=4; score=0.406185; ----agcAACAAAaa---- ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 0 0 0 0 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 0 0 0 0 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 0 0 0 0 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72 0 0 0 0

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; positions_6nt_m1 versus oligos_6nt_mkv3_m4; m=9/9; ncol2=16; w=-8; offset=-8; strand=D; shift=0; score=0.404758; aaaGAGCAAcAAAAAG--- ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 0 0 0 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 0 0 0 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 0 0 0 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -raACTAAAAyr ; Alignment reference a 0 77 117 228 24 0 207 166 187 224 50 99 c 0 35 28 0 201 1 0 25 1 0 67 25 g 0 79 32 0 1 3 18 6 5 3 42 75 t 0 37 51 0 2 224 3 31 35 1 69 29

oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score= 1; -raACTAAAAyr ; cor=; Ncor= a 0 77 117 228 24 0 207 166 187 224 50 99 c 0 35 28 0 201 1 0 25 1 0 67 25 g 0 79 32 0 1 3 18 6 5 3 42 75 t 0 37 51 0 2 224 3 31 35 1 69 29

positions_7nt_m2_shift0 (positions_7nt_m2)
; oligos_7nt_mkv4_m3 versus positions_7nt_m2; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.587849; rcAACAAAAar- ; cor=; Ncor= a 147 67 454 456 0 403 426 434 455 229 151 0 c 61 214 0 1 438 0 5 0 0 103 31 0 g 216 62 2 0 0 13 0 0 0 51 220 0 t 33 114 1 0 19 41 26 23 2 74 55 0

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift8 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift8 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=11; shift=8; ncol=19; --------AyAAAAAGGma ; Alignment reference a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 1 164 282 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 0 213 78 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 518 57 33 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0 0 85 126

positions_7nt_m1_shift8 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/9; ncol2=11; w=0; offset=0; strand=D; shift=8; score= 1; --------AyAAAAAGGma ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 1 164 282 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 0 213 78 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 518 57 33 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0 0 85 126

positions_6nt_m1_shift8 (positions_6nt_m1)
; positions_7nt_m1 versus positions_6nt_m1; m=2/9; ncol2=11; w=0; offset=0; strand=D; shift=8; score=0.999959; --------AyAAAAAGGma ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 1 165 287 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 0 214 79 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 524 58 32 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0 0 88 127

oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)
; positions_7nt_m1 versus oligos_7nt_mkv4_m1; m=3/9; ncol2=13; w=0; offset=0; strand=D; shift=8; score=0.821285; --------acAAAAAGGCA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 348 129 525 504 526 518 470 44 28 96 448 c 0 0 0 0 0 0 0 0 69 176 0 12 0 10 13 4 4 394 17 g 0 0 0 0 0 0 0 0 91 118 2 16 6 1 45 482 498 11 4 t 0 0 0 0 0 0 0 0 24 109 5 0 0 3 4 2 2 31 63

oligos_6nt_mkv3_m1_shift9 (oligos_6nt_mkv3_m1)
; positions_7nt_m1 versus oligos_6nt_mkv3_m1; m=4/9; ncol2=12; w=0; offset=1; strand=D; shift=9; score=0.746037; ---------yaAAAAGGcw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 117 355 556 566 534 548 8 9 88 372 c 0 0 0 0 0 0 0 0 0 199 75 2 3 22 13 5 0 366 40 g 0 0 0 0 0 0 0 0 0 82 35 11 2 0 6 559 563 54 12 t 0 0 0 0 0 0 0 0 0 174 107 3 1 16 5 0 0 64 148

positions_7nt_m2_shift5 (positions_7nt_m2)
; positions_7nt_m1 versus positions_7nt_m2; m=5/9; ncol2=11; w=-3; offset=-3; strand=D; shift=5; score=0.49067; -----rcAACAAAAar--- ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 0 0 0 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 0 0 0 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 0 0 0 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55 0 0 0

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; positions_7nt_m1 versus oligos_7nt_mkv4_m2; m=6/9; ncol2=14; w=-6; offset=-6; strand=D; shift=2; score=0.443444; --arAGCAACAAAAaG--- ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 0 0 0 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 0 0 0 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 0 0 0 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36 0 0 0

oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)
; positions_7nt_m1 versus oligos_6nt_mkv3_m2; m=7/9; ncol2=15; w=-7; offset=-7; strand=D; shift=1; score=0.418459; -aarAGCAACAAAAag--- ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 0 0 0 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 0 0 0 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 0 0 0 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41 0 0 0

positions_6nt_m2_shift4 (positions_6nt_m2)
; positions_7nt_m1 versus positions_6nt_m2; m=8/9; ncol2=11; w=-4; offset=-4; strand=D; shift=4; score=0.407036; ----agcAACAAAaa---- ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 0 0 0 0 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 0 0 0 0 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 0 0 0 0 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72 0 0 0 0

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; positions_7nt_m1 versus oligos_6nt_mkv3_m4; m=9/9; ncol2=16; w=-8; offset=-8; strand=D; shift=0; score=0.405195; aaaGAGCAAcAAAAAG--- ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 0 0 0 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 0 0 0 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 0 0 0 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=16; shift=0; ncol=16; aaaGAGCAAcAAAAAG ; Alignment reference a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/8; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; aaaGAGCAAcAAAAAG ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m2; m=2/8; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.920964; -aarAGCAACAAAAag ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m2; m=3/8; ncol2=14; w=0; offset=2; strand=D; shift=2; score=0.869473; --arAGCAACAAAAaG ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36
positions_7nt_m2_shift5 (positions_7nt_m2)				; oligos_6nt_mkv3_m4 versus positions_7nt_m2; m=4/8; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.629085; -----rcAACAAAAar ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55
positions_6nt_m2_shift4 (positions_6nt_m2)				; oligos_6nt_mkv3_m4 versus positions_6nt_m2; m=5/8; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.628839; ----agcAACAAAaa- ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 0 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 0 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 0 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72 0
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m3; m=6/8; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.499378; ----armAAGAAAra- ; cor=; Ncor= a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 0 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 0 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 0 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111 0
positions_7nt_m1_shift8 (positions_7nt_m1)				; oligos_6nt_mkv3_m4 versus positions_7nt_m1; m=7/8; ncol2=11; w=0; offset=8; strand=D; shift=8; score=0.405195; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0
positions_6nt_m1_shift8 (positions_6nt_m1)				; oligos_6nt_mkv3_m4 versus positions_6nt_m1; m=8/8; ncol2=11; w=0; offset=8; strand=D; shift=8; score=0.404758; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=14; shift=2; ncol=16; --arAGCAACAAAAaG ; Alignment reference a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/8; ncol2=14; w=0; offset=0; strand=D; shift=2; score= 1; --arAGCAACAAAAaG ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m2; m=2/8; ncol2=15; w=-1; offset=-1; strand=D; shift=1; score=0.927077; -aarAGCAACAAAAag ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m4; m=3/8; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.869473; aaaGAGCAAcAAAAAG ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32
positions_7nt_m2_shift5 (positions_7nt_m2)				; oligos_7nt_mkv4_m2 versus positions_7nt_m2; m=4/8; ncol2=11; w=0; offset=3; strand=D; shift=5; score=0.729885; -----rcAACAAAAar ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55
positions_6nt_m2_shift4 (positions_6nt_m2)				; oligos_7nt_mkv4_m2 versus positions_6nt_m2; m=5/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.724624; ----agcAACAAAaa- ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 0 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 0 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 0 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72 0
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m3; m=6/8; ncol2=11; w=0; offset=2; strand=D; shift=4; score=0.566341; ----armAAGAAAra- ; cor=; Ncor= a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 0 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 0 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 0 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111 0
positions_7nt_m1_shift8 (positions_7nt_m1)				; oligos_7nt_mkv4_m2 versus positions_7nt_m1; m=7/8; ncol2=11; w=0; offset=6; strand=D; shift=8; score=0.443444; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0
positions_6nt_m1_shift8 (positions_6nt_m1)				; oligos_7nt_mkv4_m2 versus positions_6nt_m1; m=8/8; ncol2=11; w=0; offset=6; strand=D; shift=8; score=0.44284; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=15; shift=1; ncol=16; -aarAGCAACAAAAag ; Alignment reference a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/8; ncol2=15; w=0; offset=0; strand=D; shift=1; score= 1; -aarAGCAACAAAAag ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m2 versus oligos_7nt_mkv4_m2; m=2/8; ncol2=14; w=0; offset=1; strand=D; shift=2; score=0.927077; --arAGCAACAAAAaG ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m4; m=3/8; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.920964; aaaGAGCAAcAAAAAG ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32
positions_7nt_m2_shift5 (positions_7nt_m2)				; oligos_6nt_mkv3_m2 versus positions_7nt_m2; m=4/8; ncol2=11; w=0; offset=4; strand=D; shift=5; score=0.68614; -----rcAACAAAAar ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55
positions_6nt_m2_shift4 (positions_6nt_m2)				; oligos_6nt_mkv3_m2 versus positions_6nt_m2; m=5/8; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.672963; ----agcAACAAAaa- ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 0 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 0 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 0 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72 0
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m3; m=6/8; ncol2=11; w=0; offset=3; strand=D; shift=4; score=0.523115; ----armAAGAAAra- ; cor=; Ncor= a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 0 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 0 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 0 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111 0
positions_7nt_m1_shift8 (positions_7nt_m1)				; oligos_6nt_mkv3_m2 versus positions_7nt_m1; m=7/8; ncol2=11; w=0; offset=7; strand=D; shift=8; score=0.418459; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0
positions_6nt_m1_shift8 (positions_6nt_m1)				; oligos_6nt_mkv3_m2 versus positions_6nt_m1; m=8/8; ncol2=11; w=0; offset=7; strand=D; shift=8; score=0.417936; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift4 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=11; shift=4; ncol=15; ----agcAACAAAaa ; Alignment reference a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72
positions_6nt_m2_shift4 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----agcAACAAAaa ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72
positions_7nt_m2_shift5 (positions_7nt_m2)				; positions_6nt_m2 versus positions_7nt_m2; m=2/8; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.803346; -----rcAACAAAAa ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; positions_6nt_m2 versus oligos_6nt_mkv3_m3; m=3/8; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.759816; ----armAAGAAAra ; cor=; Ncor= a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; positions_6nt_m2 versus oligos_7nt_mkv4_m2; m=4/8; ncol2=14; w=-2; offset=-2; strand=D; shift=2; score=0.724624; --arAGCAACAAAAa ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; positions_6nt_m2 versus oligos_6nt_mkv3_m2; m=5/8; ncol2=15; w=-3; offset=-3; strand=D; shift=1; score=0.672963; -aarAGCAACAAAAa ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; positions_6nt_m2 versus oligos_6nt_mkv3_m4; m=6/8; ncol2=16; w=-4; offset=-4; strand=D; shift=0; score=0.628839; aaaGAGCAAcAAAAA ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56
positions_7nt_m1_shift8 (positions_7nt_m1)				; positions_6nt_m2 versus positions_7nt_m1; m=7/8; ncol2=11; w=0; offset=4; strand=D; shift=8; score=0.407036; --------AyAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0
positions_6nt_m1_shift8 (positions_6nt_m1)				; positions_6nt_m2 versus positions_6nt_m1; m=8/8; ncol2=11; w=0; offset=4; strand=D; shift=8; score=0.406185; --------AyAAAAA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=13; shift=3; ncol=16; ---acAAAAAGGCAaa ; Alignment reference a 0 0 0 348 129 525 504 526 518 470 44 28 96 448 250 179 c 0 0 0 69 176 0 12 0 10 13 4 4 394 17 57 121 g 0 0 0 91 118 2 16 6 1 45 482 498 11 4 129 123 t 0 0 0 24 109 5 0 0 3 4 2 2 31 63 96 109
oligos_7nt_mkv4_m1_shift3 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/5; ncol2=13; w=0; offset=0; strand=D; shift=3; score= 1; ---acAAAAAGGCAaa ; cor=; Ncor= a 0 0 0 348 129 525 504 526 518 470 44 28 96 448 250 179 c 0 0 0 69 176 0 12 0 10 13 4 4 394 17 57 121 g 0 0 0 91 118 2 16 6 1 45 482 498 11 4 129 123 t 0 0 0 24 109 5 0 0 3 4 2 2 31 63 96 109
oligos_6nt_mkv3_m1_shift4 (oligos_6nt_mkv3_m1)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m1; m=2/5; ncol2=12; w=0; offset=1; strand=D; shift=4; score=0.892921; ----yaAAAAGGcwdd ; cor=; Ncor= a 0 0 0 0 117 355 556 566 534 548 8 9 88 372 194 174 c 0 0 0 0 199 75 2 3 22 13 5 0 366 40 50 101 g 0 0 0 0 82 35 11 2 0 6 559 563 54 12 147 150 t 0 0 0 0 174 107 3 1 16 5 0 0 64 148 181 147
positions_7nt_m1_shift3 (positions_7nt_m1)				; oligos_7nt_mkv4_m1 versus positions_7nt_m1; m=3/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.821285; ---AyAAAAAGGma-- ; cor=; Ncor= a 0 0 0 367 97 518 499 506 511 502 0 1 164 282 0 0 c 0 0 0 65 205 0 5 1 0 16 10 0 213 78 0 0 g 0 0 0 75 76 0 0 2 0 1 509 518 57 33 0 0 t 0 0 0 12 141 1 15 10 8 0 0 0 85 126 0 0
positions_6nt_m1_shift3 (positions_6nt_m1)				; oligos_7nt_mkv4_m1 versus positions_6nt_m1; m=4/5; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.821267; ---AyAAAAAGGma-- ; cor=; Ncor= a 0 0 0 370 100 517 505 512 517 509 0 1 165 287 0 0 c 0 0 0 65 205 0 5 1 0 16 10 0 214 79 0 0 g 0 0 0 76 76 0 0 2 0 0 515 524 58 32 0 0 t 0 0 0 14 144 8 15 10 8 0 0 0 88 127 0 0
positions_7nt_m2_shift0 (positions_7nt_m2)				; oligos_7nt_mkv4_m1 versus positions_7nt_m2; m=5/5; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.428388; rcAACAAAAar----- ; cor=; Ncor= a 147 67 454 456 0 403 426 434 455 229 151 0 0 0 0 0 c 61 214 0 1 438 0 5 0 0 103 31 0 0 0 0 0 g 216 62 2 0 0 13 0 0 0 51 220 0 0 0 0 0 t 33 114 1 0 19 41 26 23 2 74 55 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -yaAAAAGGcwdd ; Alignment reference a 0 117 355 556 566 534 548 8 9 88 372 194 174 c 0 199 75 2 3 22 13 5 0 366 40 50 101 g 0 82 35 11 2 0 6 559 563 54 12 147 150 t 0 174 107 3 1 16 5 0 0 64 148 181 147
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=1; score= 1; -yaAAAAGGcwdd ; cor=; Ncor= a 0 117 355 556 566 534 548 8 9 88 372 194 174 c 0 199 75 2 3 22 13 5 0 366 40 50 101 g 0 82 35 11 2 0 6 559 563 54 12 147 150 t 0 174 107 3 1 16 5 0 0 64 148 181 147
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_6nt_mkv3_m1 versus oligos_7nt_mkv4_m1; m=2/4; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.892921; acAAAAAGGCAaa ; cor=; Ncor= a 348 129 525 504 526 518 470 44 28 96 448 250 179 c 69 176 0 12 0 10 13 4 4 394 17 57 121 g 91 118 2 16 6 1 45 482 498 11 4 129 123 t 24 109 5 0 0 3 4 2 2 31 63 96 109
positions_6nt_m1_shift0 (positions_6nt_m1)				; oligos_6nt_mkv3_m1 versus positions_6nt_m1; m=3/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.747084; AyAAAAAGGma-- ; cor=; Ncor= a 370 100 517 505 512 517 509 0 1 165 287 0 0 c 65 205 0 5 1 0 16 10 0 214 79 0 0 g 76 76 0 0 2 0 0 515 524 58 32 0 0 t 14 144 8 15 10 8 0 0 0 88 127 0 0
positions_7nt_m1_shift0 (positions_7nt_m1)				; oligos_6nt_mkv3_m1 versus positions_7nt_m1; m=4/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.746037; AyAAAAAGGma-- ; cor=; Ncor= a 367 97 518 499 506 511 502 0 1 164 282 0 0 c 65 205 0 5 1 0 16 10 0 213 78 0 0 g 75 76 0 0 2 0 1 509 518 57 33 0 0 t 12 141 1 15 10 8 0 0 0 85 126 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift5 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=11; shift=5; ncol=16; -----rcAACAAAAar ; Alignment reference a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55
positions_7nt_m2_shift5 (positions_7nt_m2)				; positions_7nt_m2 versus positions_7nt_m2; m=1/10; ncol2=11; w=0; offset=0; strand=D; shift=5; score= 1; -----rcAACAAAAar ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55
positions_6nt_m2_shift4 (positions_6nt_m2)				; positions_7nt_m2 versus positions_6nt_m2; m=2/10; ncol2=11; w=-1; offset=-1; strand=D; shift=4; score=0.803346; ----agcAACAAAaa- ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 0 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 0 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 0 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72 0
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; positions_7nt_m2 versus oligos_7nt_mkv4_m2; m=3/10; ncol2=14; w=-3; offset=-3; strand=D; shift=2; score=0.729885; --arAGCAACAAAAaG ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; positions_7nt_m2 versus oligos_6nt_mkv3_m2; m=4/10; ncol2=15; w=-4; offset=-4; strand=D; shift=1; score=0.68614; -aarAGCAACAAAAag ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; positions_7nt_m2 versus oligos_6nt_mkv3_m4; m=5/10; ncol2=16; w=-5; offset=-5; strand=D; shift=0; score=0.629085; aaaGAGCAAcAAAAAG ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; positions_7nt_m2 versus oligos_6nt_mkv3_m3; m=6/10; ncol2=11; w=-1; offset=-1; strand=D; shift=4; score=0.619786; ----armAAGAAAra- ; cor=; Ncor= a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 0 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 0 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 0 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111 0
oligos_7nt_mkv4_m3_shift6 (oligos_7nt_mkv4_m3)				; positions_7nt_m2 versus oligos_7nt_mkv4_m3; m=7/10; ncol2=11; w=0; offset=1; strand=D; shift=6; score=0.587849; ------raACTAAAAy ; cor=; Ncor= a 0 0 0 0 0 0 77 117 228 24 0 207 166 187 224 50 c 0 0 0 0 0 0 35 28 0 201 1 0 25 1 0 67 g 0 0 0 0 0 0 79 32 0 1 3 18 6 5 3 42 t 0 0 0 0 0 0 37 51 0 2 224 3 31 35 1 69
positions_7nt_m1_shift8 (positions_7nt_m1)				; positions_7nt_m2 versus positions_7nt_m1; m=8/10; ncol2=11; w=0; offset=3; strand=D; shift=8; score=0.49067; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0
positions_6nt_m1_shift8 (positions_6nt_m1)				; positions_7nt_m2 versus positions_6nt_m1; m=9/10; ncol2=11; w=0; offset=3; strand=D; shift=8; score=0.489966; --------AyAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0
oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)				; positions_7nt_m2 versus oligos_7nt_mkv4_m1; m=10/10; ncol2=13; w=0; offset=3; strand=D; shift=8; score=0.428388; --------acAAAAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 348 129 525 504 526 518 470 44 c 0 0 0 0 0 0 0 0 69 176 0 12 0 10 13 4 g 0 0 0 0 0 0 0 0 91 118 2 16 6 1 45 482 t 0 0 0 0 0 0 0 0 24 109 5 0 0 3 4 2

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=11; shift=4; ncol=15; ----armAAGAAAra ; Alignment reference a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111
oligos_6nt_mkv3_m3_shift4 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score= 1; ----armAAGAAAra ; cor=; Ncor= a 0 0 0 0 217 243 227 526 549 0 545 549 550 273 250 c 0 0 0 0 98 67 183 0 1 0 0 1 0 63 76 g 0 0 0 0 131 166 103 24 0 540 0 0 0 167 113 t 0 0 0 0 104 74 37 0 0 10 5 0 0 47 111
positions_6nt_m2_shift4 (positions_6nt_m2)				; oligos_6nt_mkv3_m3 versus positions_6nt_m2; m=2/6; ncol2=11; w=0; offset=0; strand=D; shift=4; score=0.759816; ----agcAACAAAaa ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72
positions_7nt_m2_shift5 (positions_7nt_m2)				; oligos_6nt_mkv3_m3 versus positions_7nt_m2; m=3/6; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.619786; -----rcAACAAAAa ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2; m=4/6; ncol2=14; w=-2; offset=-2; strand=D; shift=2; score=0.566341; --arAGCAACAAAAa ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m2; m=5/6; ncol2=15; w=-3; offset=-3; strand=D; shift=1; score=0.523115; -aarAGCAACAAAAa ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m4; m=6/6; ncol2=16; w=-4; offset=-4; strand=D; shift=0; score=0.499378; aaaGAGCAAcAAAAA ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift8 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=11; shift=8; ncol=19; --------AyAAAAAGGma ; Alignment reference a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 1 165 287 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 0 214 79 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 524 58 32 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0 0 88 127
positions_6nt_m1_shift8 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/9; ncol2=11; w=0; offset=0; strand=D; shift=8; score= 1; --------AyAAAAAGGma ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 1 165 287 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 0 214 79 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 524 58 32 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0 0 88 127
positions_7nt_m1_shift8 (positions_7nt_m1)				; positions_6nt_m1 versus positions_7nt_m1; m=2/9; ncol2=11; w=0; offset=0; strand=D; shift=8; score=0.999959; --------AyAAAAAGGma ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 1 164 282 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 0 213 78 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 518 57 33 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0 0 85 126
oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)				; positions_6nt_m1 versus oligos_7nt_mkv4_m1; m=3/9; ncol2=13; w=0; offset=0; strand=D; shift=8; score=0.821267; --------acAAAAAGGCA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 348 129 525 504 526 518 470 44 28 96 448 c 0 0 0 0 0 0 0 0 69 176 0 12 0 10 13 4 4 394 17 g 0 0 0 0 0 0 0 0 91 118 2 16 6 1 45 482 498 11 4 t 0 0 0 0 0 0 0 0 24 109 5 0 0 3 4 2 2 31 63
oligos_6nt_mkv3_m1_shift9 (oligos_6nt_mkv3_m1)				; positions_6nt_m1 versus oligos_6nt_mkv3_m1; m=4/9; ncol2=12; w=0; offset=1; strand=D; shift=9; score=0.747084; ---------yaAAAAGGcw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 117 355 556 566 534 548 8 9 88 372 c 0 0 0 0 0 0 0 0 0 199 75 2 3 22 13 5 0 366 40 g 0 0 0 0 0 0 0 0 0 82 35 11 2 0 6 559 563 54 12 t 0 0 0 0 0 0 0 0 0 174 107 3 1 16 5 0 0 64 148
positions_7nt_m2_shift5 (positions_7nt_m2)				; positions_6nt_m1 versus positions_7nt_m2; m=5/9; ncol2=11; w=-3; offset=-3; strand=D; shift=5; score=0.489966; -----rcAACAAAAar--- ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 0 0 0 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 0 0 0 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 0 0 0 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55 0 0 0
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; positions_6nt_m1 versus oligos_7nt_mkv4_m2; m=6/9; ncol2=14; w=-6; offset=-6; strand=D; shift=2; score=0.44284; --arAGCAACAAAAaG--- ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 0 0 0 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 0 0 0 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 0 0 0 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36 0 0 0
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; positions_6nt_m1 versus oligos_6nt_mkv3_m2; m=7/9; ncol2=15; w=-7; offset=-7; strand=D; shift=1; score=0.417936; -aarAGCAACAAAAag--- ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 0 0 0 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 0 0 0 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 0 0 0 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41 0 0 0
positions_6nt_m2_shift4 (positions_6nt_m2)				; positions_6nt_m1 versus positions_6nt_m2; m=8/9; ncol2=11; w=-4; offset=-4; strand=D; shift=4; score=0.406185; ----agcAACAAAaa---- ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 0 0 0 0 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 0 0 0 0 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 0 0 0 0 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72 0 0 0 0
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; positions_6nt_m1 versus oligos_6nt_mkv3_m4; m=9/9; ncol2=16; w=-8; offset=-8; strand=D; shift=0; score=0.404758; aaaGAGCAAcAAAAAG--- ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 0 0 0 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 0 0 0 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 0 0 0 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m1_shift8 (positions_7nt_m1)				; positions_7nt_m1; m=0 (reference); ncol1=11; shift=8; ncol=19; --------AyAAAAAGGma ; Alignment reference a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 1 164 282 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 0 213 78 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 518 57 33 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0 0 85 126
positions_7nt_m1_shift8 (positions_7nt_m1)				; positions_7nt_m1 versus positions_7nt_m1; m=1/9; ncol2=11; w=0; offset=0; strand=D; shift=8; score= 1; --------AyAAAAAGGma ; cor=; Ncor= a 0 0 0 0 0 0 0 0 367 97 518 499 506 511 502 0 1 164 282 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 0 213 78 g 0 0 0 0 0 0 0 0 75 76 0 0 2 0 1 509 518 57 33 t 0 0 0 0 0 0 0 0 12 141 1 15 10 8 0 0 0 85 126
positions_6nt_m1_shift8 (positions_6nt_m1)				; positions_7nt_m1 versus positions_6nt_m1; m=2/9; ncol2=11; w=0; offset=0; strand=D; shift=8; score=0.999959; --------AyAAAAAGGma ; cor=; Ncor= a 0 0 0 0 0 0 0 0 370 100 517 505 512 517 509 0 1 165 287 c 0 0 0 0 0 0 0 0 65 205 0 5 1 0 16 10 0 214 79 g 0 0 0 0 0 0 0 0 76 76 0 0 2 0 0 515 524 58 32 t 0 0 0 0 0 0 0 0 14 144 8 15 10 8 0 0 0 88 127
oligos_7nt_mkv4_m1_shift8 (oligos_7nt_mkv4_m1)				; positions_7nt_m1 versus oligos_7nt_mkv4_m1; m=3/9; ncol2=13; w=0; offset=0; strand=D; shift=8; score=0.821285; --------acAAAAAGGCA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 348 129 525 504 526 518 470 44 28 96 448 c 0 0 0 0 0 0 0 0 69 176 0 12 0 10 13 4 4 394 17 g 0 0 0 0 0 0 0 0 91 118 2 16 6 1 45 482 498 11 4 t 0 0 0 0 0 0 0 0 24 109 5 0 0 3 4 2 2 31 63
oligos_6nt_mkv3_m1_shift9 (oligos_6nt_mkv3_m1)				; positions_7nt_m1 versus oligos_6nt_mkv3_m1; m=4/9; ncol2=12; w=0; offset=1; strand=D; shift=9; score=0.746037; ---------yaAAAAGGcw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 117 355 556 566 534 548 8 9 88 372 c 0 0 0 0 0 0 0 0 0 199 75 2 3 22 13 5 0 366 40 g 0 0 0 0 0 0 0 0 0 82 35 11 2 0 6 559 563 54 12 t 0 0 0 0 0 0 0 0 0 174 107 3 1 16 5 0 0 64 148
positions_7nt_m2_shift5 (positions_7nt_m2)				; positions_7nt_m1 versus positions_7nt_m2; m=5/9; ncol2=11; w=-3; offset=-3; strand=D; shift=5; score=0.49067; -----rcAACAAAAar--- ; cor=; Ncor= a 0 0 0 0 0 147 67 454 456 0 403 426 434 455 229 151 0 0 0 c 0 0 0 0 0 61 214 0 1 438 0 5 0 0 103 31 0 0 0 g 0 0 0 0 0 216 62 2 0 0 13 0 0 0 51 220 0 0 0 t 0 0 0 0 0 33 114 1 0 19 41 26 23 2 74 55 0 0 0
oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)				; positions_7nt_m1 versus oligos_7nt_mkv4_m2; m=6/9; ncol2=14; w=-6; offset=-6; strand=D; shift=2; score=0.443444; --arAGCAACAAAAaG--- ; cor=; Ncor= a 0 0 338 167 467 31 1 490 493 39 531 467 493 530 337 95 0 0 0 c 0 0 38 5 7 28 477 3 1 381 0 56 10 1 20 17 0 0 0 g 0 0 45 338 38 470 43 0 34 66 0 6 16 0 87 383 0 0 0 t 0 0 110 21 19 2 10 38 3 45 0 2 12 0 87 36 0 0 0
oligos_6nt_mkv3_m2_shift1 (oligos_6nt_mkv3_m2)				; positions_7nt_m1 versus oligos_6nt_mkv3_m2; m=7/9; ncol2=15; w=-7; offset=-7; strand=D; shift=1; score=0.418459; -aarAGCAACAAAAag--- ; cor=; Ncor= a 0 305 337 251 508 29 42 484 447 28 517 452 508 521 345 104 0 0 0 c 0 64 50 1 2 30 428 3 1 390 1 62 2 1 34 27 0 0 0 g 0 94 37 269 10 466 49 0 36 61 0 9 0 2 73 353 0 0 0 t 0 62 101 4 5 0 6 38 41 46 7 2 15 1 73 41 0 0 0
positions_6nt_m2_shift4 (positions_6nt_m2)				; positions_7nt_m1 versus positions_6nt_m2; m=8/9; ncol2=11; w=-4; offset=-4; strand=D; shift=4; score=0.407036; ----agcAACAAAaa---- ; cor=; Ncor= a 0 0 0 0 243 104 75 396 425 0 416 418 413 258 243 0 0 0 0 c 0 0 0 0 59 98 286 25 0 415 0 1 4 81 50 0 0 0 0 g 0 0 0 0 62 167 17 1 0 0 7 0 0 32 60 0 0 0 0 t 0 0 0 0 61 56 47 3 0 10 2 6 8 54 72 0 0 0 0
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; positions_7nt_m1 versus oligos_6nt_mkv3_m4; m=9/9; ncol2=16; w=-8; offset=-8; strand=D; shift=0; score=0.405195; aaaGAGCAAcAAAAAG--- ; cor=; Ncor= a 287 358 361 111 484 15 17 531 493 47 530 460 500 514 371 70 0 0 0 c 94 40 27 1 0 33 478 4 6 340 1 18 9 22 20 12 0 0 0 g 77 85 46 421 38 487 40 0 37 66 0 42 23 0 89 422 0 0 0 t 78 53 102 3 14 1 1 1 0 83 5 16 4 0 56 32 0 0 0