One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/12/18/peak-motifs.2025-12-18.171557_2025-12-18.171557_4Sppd9/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/2025/12/18/peak-motifs.2025-12-18.171557_2025-12-18.171557_4Sppd9/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; gATTCCATTCgATkmy ; Alignment reference a 300 2123 111 84 46 54 2351 30 49 84 299 2310 121 159 967 165 c 607 90 47 44 2352 2129 45 43 40 2076 567 40 98 51 1184 1011 g 1404 125 219 36 61 251 95 30 34 50 1547 88 260 977 114 312 t 229 202 2163 2376 81 106 49 2437 2417 330 127 102 2061 1353 275 1052

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; gATTCCATTCgATkmy ; cor=; Ncor= a 300 2123 111 84 46 54 2351 30 49 84 299 2310 121 159 967 165 c 607 90 47 44 2352 2129 45 43 40 2076 567 40 98 51 1184 1011 g 1404 125 219 36 61 251 95 30 34 50 1547 88 260 977 114 312 t 229 202 2163 2376 81 106 49 2437 2417 330 127 102 2061 1353 275 1052

oligos_6nt_mkv3_m5_rc_shift0 (oligos_6nt_mkv3_m5_rc)
; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m5_rc; m=2/3; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.869447; gATTCCATTCGATk-- ; cor=; Ncor= a 274 1660 278 47 48 24 1918 42 54 79 213 1809 185 158 0 0 c 339 60 38 13 1806 1902 12 37 22 1637 282 37 83 58 0 0 g 1232 104 197 8 85 29 31 15 21 35 1445 76 254 703 0 0 t 155 176 1487 1932 61 45 39 1906 1903 249 60 78 1478 1081 0 0

oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4; m=3/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.576402; --kwyGATTCCATT-- ; cor=; Ncor= a 0 0 213 637 60 83 1807 79 39 37 34 1801 144 124 0 0 c 0 0 111 94 1171 284 16 19 17 1795 1833 17 128 93 0 0 g 0 0 568 83 39 1513 40 172 24 50 7 75 60 118 0 0 t 0 0 1032 1110 654 44 61 1654 1844 42 50 31 1592 1589 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --atATACATATat ; Alignment reference a 0 0 1975 662 2891 99 3220 1 3115 75 3109 241 2130 728 c 0 0 295 446 106 184 60 3351 47 170 35 263 205 447 g 0 0 425 311 152 27 25 2 102 60 131 155 324 241 t 0 0 677 1953 223 3062 67 18 108 3067 97 2713 713 1956

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --atATACATATat ; cor=; Ncor= a 0 0 1975 662 2891 99 3220 1 3115 75 3109 241 2130 728 c 0 0 295 446 106 184 60 3351 47 170 35 263 205 447 g 0 0 425 311 152 27 25 2 102 60 131 155 324 241 t 0 0 677 1953 223 3062 67 18 108 3067 97 2713 713 1956

positions_7nt_m1_shift3 (positions_7nt_m1)
; oligos_6nt_mkv3_m1 versus positions_7nt_m1; m=2/3; ncol2=12; w=0; offset=1; strand=D; shift=3; score=0.68017; ---taTATATATAt ; cor=; Ncor= a 0 0 0 555 2104 6 3295 6 3303 1 3301 2 3303 376 c 0 0 0 619 238 8 14 20 0 24 1 17 11 610 g 0 0 0 428 610 11 17 1 24 0 20 14 8 238 t 0 0 0 1726 376 3303 2 3301 1 3303 6 3295 6 2104

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3; m=3/3; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.602031; atAGATAGATAdaw ; cor=; Ncor= a 1274 470 1437 63 1872 57 1881 46 1901 90 1670 725 1191 510 c 108 155 50 16 14 31 10 48 16 50 23 120 214 170 g 257 237 114 1754 44 61 37 1710 29 127 166 601 155 260 t 320 1097 358 126 29 1810 31 155 13 1692 100 513 399 1019

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; wwACTATAAww ; Alignment reference a 115 119 320 3 0 326 0 320 320 131 143 c 52 37 0 321 6 0 0 1 5 47 40 g 45 53 5 0 16 2 1 0 1 41 38 t 116 119 3 4 306 0 327 7 2 109 107

oligos_7nt_mkv4_m5_shift0 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5 versus oligos_7nt_mkv4_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 1; wwACTATAAww ; cor=; Ncor= a 115 119 320 3 0 326 0 320 320 131 143 c 52 37 0 321 6 0 0 1 5 47 40 g 45 53 5 0 16 2 1 0 1 41 38 t 116 119 3 4 306 0 327 7 2 109 107

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift2 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=14; shift=2; ncol=16; --mATCGAATGGAATc ; Alignment reference a 0 0 1081 1478 78 60 249 1903 1906 39 45 61 1932 1487 176 155 c 0 0 703 254 76 1445 35 21 15 31 29 85 8 197 104 1232 g 0 0 58 83 37 282 1637 22 37 12 1902 1806 13 38 60 339 t 0 0 158 185 1809 213 79 54 42 1918 24 48 47 278 1660 274

oligos_6nt_mkv3_m5_shift2 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=2; score= 1; --mATCGAATGGAATc ; cor=; Ncor= a 0 0 1081 1478 78 60 249 1903 1906 39 45 61 1932 1487 176 155 c 0 0 703 254 76 1445 35 21 15 31 29 85 8 197 104 1232 g 0 0 58 83 37 282 1637 22 37 12 1902 1806 13 38 60 339 t 0 0 158 185 1809 213 79 54 42 1918 24 48 47 278 1660 274

oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)
; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m1_rc; m=2/3; ncol2=16; w=-2; offset=-2; strand=R; shift=0; score=0.869447; rkmATcGAATGGAATc ; cor=; Ncor= a 1052 275 1353 2061 102 127 330 2417 2437 49 106 81 2376 2163 202 229 c 312 114 977 260 88 1547 50 34 30 95 251 61 36 219 125 1404 g 1011 1184 51 98 40 567 2076 40 43 45 2129 2352 44 47 90 607 t 165 967 159 121 2310 299 84 49 30 2351 54 46 84 111 2123 300

oligos_7nt_mkv4_m4_rc_shift2 (oligos_7nt_mkv4_m4_rc)
; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m4_rc; m=3/3; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.623518; --AATGGAATCrwm-- ; cor=; Ncor= a 0 0 1589 1592 31 50 42 1844 1654 61 44 654 1110 1032 0 0 c 0 0 118 60 75 7 50 24 172 40 1513 39 83 568 0 0 g 0 0 93 128 17 1833 1795 17 19 16 284 1171 94 111 0 0 t 0 0 124 144 1801 34 37 39 79 1807 83 60 637 213 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift5 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m4_shift5 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=10; shift=5; ncol=15; -----wwTATTAAww ; Alignment reference a 0 0 0 0 0 641 818 0 1871 0 0 1871 1871 712 815 c 0 0 0 0 0 262 224 0 0 0 0 0 0 222 216 g 0 0 0 0 0 241 230 0 0 0 0 0 0 197 245 t 0 0 0 0 0 727 599 1871 0 1871 1871 0 0 740 595

positions_6nt_m4_shift5 (positions_6nt_m4)
; positions_6nt_m4 versus positions_6nt_m4; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=5; score= 1; -----wwTATTAAww ; cor=; Ncor= a 0 0 0 0 0 641 818 0 1871 0 0 1871 1871 712 815 c 0 0 0 0 0 262 224 0 0 0 0 0 0 222 216 g 0 0 0 0 0 241 230 0 0 0 0 0 0 197 245 t 0 0 0 0 0 727 599 1871 0 1871 1871 0 0 740 595

positions_6nt_m2_rc_shift0 (positions_6nt_m2_rc)
; positions_6nt_m4 versus positions_6nt_m2_rc; m=2/2; ncol2=15; w=-5; offset=-5; strand=R; shift=0; score=0.478914; wwATATTTTTTAAww ; cor=; Ncor= a 238 186 419 16 456 26 52 20 16 28 54 459 463 212 190 c 51 75 10 15 3 8 10 8 11 11 13 18 4 55 44 g 51 43 21 9 11 9 5 4 4 9 11 8 6 51 68 t 148 184 38 448 18 445 421 456 457 440 410 3 15 170 186

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; atAGATAGATAdaw ; Alignment reference a 1274 470 1437 63 1872 57 1881 46 1901 90 1670 725 1191 510 c 108 155 50 16 14 31 10 48 16 50 23 120 214 170 g 257 237 114 1754 44 61 37 1710 29 127 166 601 155 260 t 320 1097 358 126 29 1810 31 155 13 1692 100 513 399 1019

oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; atAGATAGATAdaw ; cor=; Ncor= a 1274 470 1437 63 1872 57 1881 46 1901 90 1670 725 1191 510 c 108 155 50 16 14 31 10 48 16 50 23 120 214 170 g 257 237 114 1754 44 61 37 1710 29 127 166 601 155 260 t 320 1097 358 126 29 1810 31 155 13 1692 100 513 399 1019

oligos_7nt_mkv4_m2_rc_shift1 (oligos_7nt_mkv4_m2_rc)
; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2_rc; m=2/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.778447; -wAGATAGATAd-- ; cor=; Ncor= a 0 471 1204 0 1587 74 1675 4 1621 118 1235 482 0 0 c 0 113 45 0 27 32 5 2 26 61 61 145 0 0 g 0 218 81 1753 60 80 32 1731 48 104 200 607 0 0 t 0 952 424 1 80 1568 42 17 59 1471 258 520 0 0

oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1; m=3/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.602031; --atATACATATat ; cor=; Ncor= a 0 0 1975 662 2891 99 3220 1 3115 75 3109 241 2130 728 c 0 0 295 446 106 184 60 3351 47 170 35 263 205 447 g 0 0 425 311 152 27 25 2 102 60 131 155 324 241 t 0 0 677 1953 223 3062 67 18 108 3067 97 2713 713 1956

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

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; taTATATATAta ; Alignment reference a 555 2104 6 3295 6 3303 1 3301 2 3303 376 1726 c 619 238 8 14 20 0 24 1 17 11 610 428 g 428 610 11 17 1 24 0 20 14 8 238 619 t 1726 376 3303 2 3301 1 3303 6 3295 6 2104 555

positions_7nt_m1_shift0 (positions_7nt_m1)
; positions_7nt_m1 versus positions_7nt_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score= 1; taTATATATAta ; cor=; Ncor= a 555 2104 6 3295 6 3303 1 3301 2 3303 376 1726 c 619 238 8 14 20 0 24 1 17 11 610 428 g 428 610 11 17 1 24 0 20 14 8 238 619 t 1726 376 3303 2 3301 1 3303 6 3295 6 2104 555

oligos_6nt_mkv3_m1_rc_shift1 (oligos_6nt_mkv3_m1_rc)
; positions_7nt_m1 versus oligos_6nt_mkv3_m1_rc; m=2/2; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.68017; -atATATGTATa ; cor=; Ncor= a 0 1956 713 2713 97 3067 108 18 67 3062 223 1953 c 0 241 324 155 131 60 102 2 25 27 152 311 g 0 447 205 263 35 170 47 3351 60 184 106 446 t 0 728 2130 241 3109 75 3115 1 3220 99 2891 662

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; waAAGAAAAAAww ; Alignment reference a 825 874 1595 1673 1 1678 1652 1638 1616 1578 1593 826 803 c 194 199 67 7 1 37 44 43 42 69 55 177 188 g 341 310 82 70 1804 52 77 83 84 58 61 297 277 t 474 451 90 84 28 67 61 70 92 129 125 534 566

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; waAAGAAAAAAww ; cor=; Ncor= a 825 874 1595 1673 1 1678 1652 1638 1616 1578 1593 826 803 c 194 199 67 7 1 37 44 43 42 69 55 177 188 g 341 310 82 70 1804 52 77 83 84 58 61 297 277 t 474 451 90 84 28 67 61 70 92 129 125 534 566

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m4; m=2/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.71533; wwAAGAAAAcAAA ; cor=; Ncor= a 473 473 733 922 44 905 939 909 937 165 902 807 848 c 111 116 80 10 37 18 19 34 10 646 32 43 28 g 163 153 77 25 895 35 26 33 25 57 31 67 53 t 271 276 128 61 42 60 34 42 46 150 53 101 89

positions_6nt_m5_shift1 (positions_6nt_m5)
; oligos_7nt_mkv4_m3 versus positions_6nt_m5; m=3/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.703898; -wwAGAAAAww-- ; cor=; Ncor= a 0 1054 965 2287 0 2288 2287 2287 2287 967 1043 0 0 c 0 231 346 1 0 0 0 0 1 301 273 0 0 g 0 375 384 0 2288 0 0 0 0 321 328 0 0 t 0 628 593 0 0 0 1 1 0 699 644 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift5 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift5 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=14; shift=5; ncol=19; -----wwTTAAAAATAAww ; Alignment reference a 0 0 0 0 0 471 412 93 70 1057 1103 1135 1127 1104 68 1067 1029 516 466 c 0 0 0 0 0 133 149 26 34 36 12 14 19 21 27 28 45 152 151 g 0 0 0 0 0 153 132 33 28 29 37 12 8 25 36 25 16 147 157 t 0 0 0 0 0 435 499 1040 1060 70 40 31 38 42 1061 72 102 377 418

positions_6nt_m3_shift5 (positions_6nt_m3)
; positions_6nt_m3 versus positions_6nt_m3; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=5; score= 1; -----wwTTAAAAATAAww ; cor=; Ncor= a 0 0 0 0 0 471 412 93 70 1057 1103 1135 1127 1104 68 1067 1029 516 466 c 0 0 0 0 0 133 149 26 34 36 12 14 19 21 27 28 45 152 151 g 0 0 0 0 0 153 132 33 28 29 37 12 8 25 36 25 16 147 157 t 0 0 0 0 0 435 499 1040 1060 70 40 31 38 42 1061 72 102 377 418

positions_6nt_m1_shift5 (positions_6nt_m1)
; positions_6nt_m3 versus positions_6nt_m1; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=5; score=0.891315; -----wwTTAAAAATATww ; cor=; Ncor= a 0 0 0 0 0 403 352 60 47 995 1045 1080 1069 1059 59 1024 74 428 386 c 0 0 0 0 0 138 143 17 27 41 18 19 14 19 24 23 42 121 136 g 0 0 0 0 0 133 124 22 30 28 32 14 11 18 19 37 16 180 117 t 0 0 0 0 0 476 531 1051 1046 86 55 37 56 54 1048 66 1018 421 511

positions_6nt_m2_shift4 (positions_6nt_m2)
; positions_6nt_m3 versus positions_6nt_m2; m=3/4; ncol2=15; w=-1; offset=-1; strand=D; shift=4; score=0.719522; ----wwTTAAAAAATATww ; cor=; Ncor= a 0 0 0 0 186 170 15 3 410 440 457 456 421 445 18 448 38 184 148 c 0 0 0 0 68 51 6 8 11 9 4 4 5 9 11 9 21 43 51 g 0 0 0 0 44 55 4 18 13 11 11 8 10 8 3 15 10 75 51 t 0 0 0 0 190 212 463 459 54 28 16 20 52 26 456 16 419 186 238

oligos_6nt_mkv3_m2_rc_shift0 (oligos_6nt_mkv3_m2_rc)
; positions_6nt_m3 versus oligos_6nt_mkv3_m2_rc; m=4/4; ncol2=20; w=-5; offset=-5; strand=R; shift=0; score=0.584975; wwTTTATTTTAAAATAAAw ; cor=; Ncor= a 130 123 55 43 37 281 20 37 34 35 275 290 281 294 24 280 272 242 127 c 29 33 25 6 9 13 9 9 6 20 7 5 7 12 18 10 16 14 53 g 35 54 14 16 10 18 12 7 5 7 20 7 10 9 13 9 6 25 33 t 142 126 242 271 280 24 295 283 291 274 34 34 38 21 281 37 42 55 123

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift5 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift5 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=14; shift=5; ncol=19; -----wwTTAAAAATATww ; Alignment reference a 0 0 0 0 0 403 352 60 47 995 1045 1080 1069 1059 59 1024 74 428 386 c 0 0 0 0 0 138 143 17 27 41 18 19 14 19 24 23 42 121 136 g 0 0 0 0 0 133 124 22 30 28 32 14 11 18 19 37 16 180 117 t 0 0 0 0 0 476 531 1051 1046 86 55 37 56 54 1048 66 1018 421 511

positions_6nt_m1_shift5 (positions_6nt_m1)
; positions_6nt_m1 versus positions_6nt_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=5; score= 1; -----wwTTAAAAATATww ; cor=; Ncor= a 0 0 0 0 0 403 352 60 47 995 1045 1080 1069 1059 59 1024 74 428 386 c 0 0 0 0 0 138 143 17 27 41 18 19 14 19 24 23 42 121 136 g 0 0 0 0 0 133 124 22 30 28 32 14 11 18 19 37 16 180 117 t 0 0 0 0 0 476 531 1051 1046 86 55 37 56 54 1048 66 1018 421 511

positions_6nt_m3_shift5 (positions_6nt_m3)
; positions_6nt_m1 versus positions_6nt_m3; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=5; score=0.891315; -----wwTTAAAAATAAww ; cor=; Ncor= a 0 0 0 0 0 471 412 93 70 1057 1103 1135 1127 1104 68 1067 1029 516 466 c 0 0 0 0 0 133 149 26 34 36 12 14 19 21 27 28 45 152 151 g 0 0 0 0 0 153 132 33 28 29 37 12 8 25 36 25 16 147 157 t 0 0 0 0 0 435 499 1040 1060 70 40 31 38 42 1061 72 102 377 418

positions_6nt_m2_shift4 (positions_6nt_m2)
; positions_6nt_m1 versus positions_6nt_m2; m=3/4; ncol2=15; w=-1; offset=-1; strand=D; shift=4; score=0.814132; ----wwTTAAAAAATATww ; cor=; Ncor= a 0 0 0 0 186 170 15 3 410 440 457 456 421 445 18 448 38 184 148 c 0 0 0 0 68 51 6 8 11 9 4 4 5 9 11 9 21 43 51 g 0 0 0 0 44 55 4 18 13 11 11 8 10 8 3 15 10 75 51 t 0 0 0 0 190 212 463 459 54 28 16 20 52 26 456 16 419 186 238

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; positions_6nt_m1 versus oligos_6nt_mkv3_m2; m=4/4; ncol2=20; w=-5; offset=-5; strand=D; shift=0; score=0.519475; wwTTTATTTTAAAATAAAw ; cor=; Ncor= a 130 123 55 42 37 281 21 38 34 34 274 291 283 295 24 280 271 242 126 c 29 33 25 6 9 13 9 10 7 20 7 5 7 12 18 10 16 14 54 g 34 53 14 16 10 18 12 7 5 7 20 6 9 9 13 9 6 25 33 t 143 127 242 272 280 24 294 281 290 275 35 34 37 20 281 37 43 55 123

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 4 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; wwAAGAAAAcAAAaww ; Alignment reference a 473 473 733 922 44 905 939 909 937 165 902 807 848 639 455 456 c 111 116 80 10 37 18 19 34 10 646 32 43 28 73 112 130 g 163 153 77 25 895 35 26 33 25 57 31 67 53 91 152 128 t 271 276 128 61 42 60 34 42 46 150 53 101 89 215 299 304

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; wwAAGAAAAcAAAaww ; cor=; Ncor= a 473 473 733 922 44 905 939 909 937 165 902 807 848 639 455 456 c 111 116 80 10 37 18 19 34 10 646 32 43 28 73 112 130 g 163 153 77 25 895 35 26 33 25 57 31 67 53 91 152 128 t 271 276 128 61 42 60 34 42 46 150 53 101 89 215 299 304

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m3; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.71533; waAAGAAAAAAww--- ; cor=; Ncor= a 825 874 1595 1673 1 1678 1652 1638 1616 1578 1593 826 803 0 0 0 c 194 199 67 7 1 37 44 43 42 69 55 177 188 0 0 0 g 341 310 82 70 1804 52 77 83 84 58 61 297 277 0 0 0 t 474 451 90 84 28 67 61 70 92 129 125 534 566 0 0 0

positions_6nt_m5_shift1 (positions_6nt_m5)
; oligos_6nt_mkv3_m4 versus positions_6nt_m5; m=3/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.570247; -wwAGAAAAww----- ; cor=; Ncor= a 0 1054 965 2287 0 2288 2287 2287 2287 967 1043 0 0 0 0 0 c 0 231 346 1 0 0 0 0 1 301 273 0 0 0 0 0 g 0 375 384 0 2288 0 0 0 0 321 328 0 0 0 0 0 t 0 628 593 0 0 0 1 1 0 699 644 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --kwyGATTCCATT ; Alignment reference a 0 0 213 637 60 83 1807 79 39 37 34 1801 144 124 c 0 0 111 94 1171 284 16 19 17 1795 1833 17 128 93 g 0 0 568 83 39 1513 40 172 24 50 7 75 60 118 t 0 0 1032 1110 654 44 61 1654 1844 42 50 31 1592 1589

oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --kwyGATTCCATT ; cor=; Ncor= a 0 0 213 637 60 83 1807 79 39 37 34 1801 144 124 c 0 0 111 94 1171 284 16 19 17 1795 1833 17 128 93 g 0 0 568 83 39 1513 40 172 24 50 7 75 60 118 t 0 0 1032 1110 654 44 61 1654 1844 42 50 31 1592 1589

oligos_6nt_mkv3_m5_rc_shift0 (oligos_6nt_mkv3_m5_rc)
; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m5_rc; m=2/3; ncol2=14; w=-2; offset=-2; strand=R; shift=0; score=0.623518; gATTCCATTCGATk ; cor=; Ncor= a 274 1660 278 47 48 24 1918 42 54 79 213 1809 185 158 c 339 60 38 13 1806 1902 12 37 22 1637 282 37 83 58 g 1232 104 197 8 85 29 31 15 21 35 1445 76 254 703 t 155 176 1487 1932 61 45 39 1906 1903 249 60 78 1478 1081

oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)
; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m1; m=3/3; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.576402; gATTCCATTCgATk ; cor=; Ncor= a 300 2123 111 84 46 54 2351 30 49 84 299 2310 121 159 c 607 90 47 44 2352 2129 45 43 40 2076 567 40 98 51 g 1404 125 219 36 61 251 95 30 34 50 1547 88 260 977 t 229 202 2163 2376 81 106 49 2437 2417 330 127 102 2061 1353

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift2 ; 3 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=11; shift=2; ncol=13; --hTATCTATCTw ; Alignment reference a 0 0 520 258 1471 59 17 42 1568 80 1 424 952 c 0 0 607 200 104 48 1731 32 80 60 1753 81 218 g 0 0 145 61 61 26 2 5 32 27 0 45 113 t 0 0 482 1235 118 1621 4 1675 74 1587 0 1204 471

oligos_7nt_mkv4_m2_shift2 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2 versus oligos_7nt_mkv4_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=2; score= 1; --hTATCTATCTw ; cor=; Ncor= a 0 0 520 258 1471 59 17 42 1568 80 1 424 952 c 0 0 607 200 104 48 1731 32 80 60 1753 81 218 g 0 0 145 61 61 26 2 5 32 27 0 45 113 t 0 0 482 1235 118 1621 4 1675 74 1587 0 1204 471

oligos_6nt_mkv3_m3_rc_shift0 (oligos_6nt_mkv3_m3_rc)
; oligos_7nt_mkv4_m2 versus oligos_6nt_mkv3_m3_rc; m=2/2; ncol2=14; w=-2; offset=-2; strand=R; shift=0; score=0.778447; wthTATCTATCTa ; cor=; Ncor= a 1019 399 513 100 1692 13 155 31 1810 29 126 358 1097 c 260 155 601 166 127 29 1710 37 61 44 1754 114 237 g 170 214 120 23 50 16 48 10 31 14 16 50 155 t 510 1191 725 1670 90 1901 46 1881 57 1872 63 1437 470

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; wwTTTATTTTAAAATAAAww ; Alignment reference a 130 123 55 42 37 281 21 38 34 34 274 291 283 295 24 280 271 242 126 142 c 29 33 25 6 9 13 9 10 7 20 7 5 7 12 18 10 16 14 54 35 g 34 53 14 16 10 18 12 7 5 7 20 6 9 9 13 9 6 25 33 29 t 143 127 242 272 280 24 294 281 290 275 35 34 37 20 281 37 43 55 123 130

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/4; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; wwTTTATTTTAAAATAAAww ; cor=; Ncor= a 130 123 55 42 37 281 21 38 34 34 274 291 283 295 24 280 271 242 126 142 c 29 33 25 6 9 13 9 10 7 20 7 5 7 12 18 10 16 14 54 35 g 34 53 14 16 10 18 12 7 5 7 20 6 9 9 13 9 6 25 33 29 t 143 127 242 272 280 24 294 281 290 275 35 34 37 20 281 37 43 55 123 130

positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)
; oligos_6nt_mkv3_m2 versus positions_6nt_m3_rc; m=2/4; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.584975; -wwTTATTTTTAAww----- ; cor=; Ncor= a 0 418 377 102 72 1061 42 38 31 40 70 1060 1040 499 435 0 0 0 0 0 c 0 157 147 16 25 36 25 8 12 37 29 28 33 132 153 0 0 0 0 0 g 0 151 152 45 28 27 21 19 14 12 36 34 26 149 133 0 0 0 0 0 t 0 466 516 1029 1067 68 1104 1127 1135 1103 1057 70 93 412 471 0 0 0 0 0

positions_6nt_m1_shift5 (positions_6nt_m1)
; oligos_6nt_mkv3_m2 versus positions_6nt_m1; m=3/4; ncol2=14; w=0; offset=5; strand=D; shift=5; score=0.519475; -----wwTTAAAAATATww- ; cor=; Ncor= a 0 0 0 0 0 403 352 60 47 995 1045 1080 1069 1059 59 1024 74 428 386 0 c 0 0 0 0 0 138 143 17 27 41 18 19 14 19 24 23 42 121 136 0 g 0 0 0 0 0 133 124 22 30 28 32 14 11 18 19 37 16 180 117 0 t 0 0 0 0 0 476 531 1051 1046 86 55 37 56 54 1048 66 1018 421 511 0

positions_6nt_m2_shift6 (positions_6nt_m2)
; oligos_6nt_mkv3_m2 versus positions_6nt_m2; m=4/4; ncol2=15; w=0; offset=6; strand=D; shift=6; score=0.47922; ------wwTTAAAAAATATw ; cor=; Ncor= a 0 0 0 0 0 0 186 170 15 3 410 440 457 456 421 445 18 448 38 184 c 0 0 0 0 0 0 68 51 6 8 11 9 4 4 5 9 11 9 21 43 g 0 0 0 0 0 0 44 55 4 18 13 11 11 8 10 8 3 15 10 75 t 0 0 0 0 0 0 190 212 463 459 54 28 16 20 52 26 456 16 419 186

One-to-n matrix alignment; reference matrix: positions_6nt_m5_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m5_shift1 (positions_6nt_m5)
; positions_6nt_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -wwAGAAAAww ; Alignment reference a 0 1054 965 2287 0 2288 2287 2287 2287 967 1043 c 0 231 346 1 0 0 0 0 1 301 273 g 0 375 384 0 2288 0 0 0 0 321 328 t 0 628 593 0 0 0 1 1 0 699 644

positions_6nt_m5_shift1 (positions_6nt_m5)
; positions_6nt_m5 versus positions_6nt_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wwAGAAAAww ; cor=; Ncor= a 0 1054 965 2287 0 2288 2287 2287 2287 967 1043 c 0 231 346 1 0 0 0 0 1 301 273 g 0 375 384 0 2288 0 0 0 0 321 328 t 0 628 593 0 0 0 1 1 0 699 644

oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)
; positions_6nt_m5 versus oligos_7nt_mkv4_m3; m=2/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.703898; waAAGAAAAAA ; cor=; Ncor= a 825 874 1595 1673 1 1678 1652 1638 1616 1578 1593 c 194 199 67 7 1 37 44 43 42 69 55 g 341 310 82 70 1804 52 77 83 84 58 61 t 474 451 90 84 28 67 61 70 92 129 125

oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; positions_6nt_m5 versus oligos_6nt_mkv3_m4; m=3/3; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.570247; wwAAGAAAAcA ; cor=; Ncor= a 473 473 733 922 44 905 939 909 937 165 902 c 111 116 80 10 37 18 19 34 10 646 32 g 163 153 77 25 895 35 26 33 25 57 31 t 271 276 128 61 42 60 34 42 46 150 53

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift6 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift6 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=15; shift=6; ncol=21; ------wwTTAAAAAATATww ; Alignment reference a 0 0 0 0 0 0 186 170 15 3 410 440 457 456 421 445 18 448 38 184 148 c 0 0 0 0 0 0 68 51 6 8 11 9 4 4 5 9 11 9 21 43 51 g 0 0 0 0 0 0 44 55 4 18 13 11 11 8 10 8 3 15 10 75 51 t 0 0 0 0 0 0 190 212 463 459 54 28 16 20 52 26 456 16 419 186 238

positions_6nt_m2_shift6 (positions_6nt_m2)
; positions_6nt_m2 versus positions_6nt_m2; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=6; score= 1; ------wwTTAAAAAATATww ; cor=; Ncor= a 0 0 0 0 0 0 186 170 15 3 410 440 457 456 421 445 18 448 38 184 148 c 0 0 0 0 0 0 68 51 6 8 11 9 4 4 5 9 11 9 21 43 51 g 0 0 0 0 0 0 44 55 4 18 13 11 11 8 10 8 3 15 10 75 51 t 0 0 0 0 0 0 190 212 463 459 54 28 16 20 52 26 456 16 419 186 238

positions_6nt_m1_shift7 (positions_6nt_m1)
; positions_6nt_m2 versus positions_6nt_m1; m=2/5; ncol2=14; w=0; offset=1; strand=D; shift=7; score=0.814132; -------wwTTAAAAATATww ; cor=; Ncor= a 0 0 0 0 0 0 0 403 352 60 47 995 1045 1080 1069 1059 59 1024 74 428 386 c 0 0 0 0 0 0 0 138 143 17 27 41 18 19 14 19 24 23 42 121 136 g 0 0 0 0 0 0 0 133 124 22 30 28 32 14 11 18 19 37 16 180 117 t 0 0 0 0 0 0 0 476 531 1051 1046 86 55 37 56 54 1048 66 1018 421 511

positions_6nt_m3_shift7 (positions_6nt_m3)
; positions_6nt_m2 versus positions_6nt_m3; m=3/5; ncol2=14; w=0; offset=1; strand=D; shift=7; score=0.719522; -------wwTTAAAAATAAww ; cor=; Ncor= a 0 0 0 0 0 0 0 471 412 93 70 1057 1103 1135 1127 1104 68 1067 1029 516 466 c 0 0 0 0 0 0 0 133 149 26 34 36 12 14 19 21 27 28 45 152 151 g 0 0 0 0 0 0 0 153 132 33 28 29 37 12 8 25 36 25 16 147 157 t 0 0 0 0 0 0 0 435 499 1040 1060 70 40 31 38 42 1061 72 102 377 418

oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)
; positions_6nt_m2 versus oligos_6nt_mkv3_m2; m=4/5; ncol2=20; w=-6; offset=-6; strand=D; shift=0; score=0.47922; wwTTTATTTTAAAATAAAww- ; cor=; Ncor= a 130 123 55 42 37 281 21 38 34 34 274 291 283 295 24 280 271 242 126 142 0 c 29 33 25 6 9 13 9 10 7 20 7 5 7 12 18 10 16 14 54 35 0 g 34 53 14 16 10 18 12 7 5 7 20 6 9 9 13 9 6 25 33 29 0 t 143 127 242 272 280 24 294 281 290 275 35 34 37 20 281 37 43 55 123 130 0

positions_6nt_m4_rc_shift6 (positions_6nt_m4_rc)
; positions_6nt_m2 versus positions_6nt_m4_rc; m=5/5; ncol2=10; w=0; offset=0; strand=R; shift=6; score=0.478914; ------wwTTAATAww----- ; cor=; Ncor= a 0 0 0 0 0 0 595 740 0 0 1871 1871 0 1871 599 727 0 0 0 0 0 c 0 0 0 0 0 0 245 197 0 0 0 0 0 0 230 241 0 0 0 0 0 g 0 0 0 0 0 0 216 222 0 0 0 0 0 0 224 262 0 0 0 0 0 t 0 0 0 0 0 0 815 712 1871 1871 0 0 1871 0 818 641 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; gATTCCATTCgATkmy ; Alignment reference a 300 2123 111 84 46 54 2351 30 49 84 299 2310 121 159 967 165 c 607 90 47 44 2352 2129 45 43 40 2076 567 40 98 51 1184 1011 g 1404 125 219 36 61 251 95 30 34 50 1547 88 260 977 114 312 t 229 202 2163 2376 81 106 49 2437 2417 330 127 102 2061 1353 275 1052
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m1; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; gATTCCATTCgATkmy ; cor=; Ncor= a 300 2123 111 84 46 54 2351 30 49 84 299 2310 121 159 967 165 c 607 90 47 44 2352 2129 45 43 40 2076 567 40 98 51 1184 1011 g 1404 125 219 36 61 251 95 30 34 50 1547 88 260 977 114 312 t 229 202 2163 2376 81 106 49 2437 2417 330 127 102 2061 1353 275 1052
oligos_6nt_mkv3_m5_rc_shift0 (oligos_6nt_mkv3_m5_rc)				; oligos_7nt_mkv4_m1 versus oligos_6nt_mkv3_m5_rc; m=2/3; ncol2=14; w=0; offset=0; strand=R; shift=0; score=0.869447; gATTCCATTCGATk-- ; cor=; Ncor= a 274 1660 278 47 48 24 1918 42 54 79 213 1809 185 158 0 0 c 339 60 38 13 1806 1902 12 37 22 1637 282 37 83 58 0 0 g 1232 104 197 8 85 29 31 15 21 35 1445 76 254 703 0 0 t 155 176 1487 1932 61 45 39 1906 1903 249 60 78 1478 1081 0 0
oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m1 versus oligos_7nt_mkv4_m4; m=3/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.576402; --kwyGATTCCATT-- ; cor=; Ncor= a 0 0 213 637 60 83 1807 79 39 37 34 1801 144 124 0 0 c 0 0 111 94 1171 284 16 19 17 1795 1833 17 128 93 0 0 g 0 0 568 83 39 1513 40 172 24 50 7 75 60 118 0 0 t 0 0 1032 1110 654 44 61 1654 1844 42 50 31 1592 1589 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --atATACATATat ; Alignment reference a 0 0 1975 662 2891 99 3220 1 3115 75 3109 241 2130 728 c 0 0 295 446 106 184 60 3351 47 170 35 263 205 447 g 0 0 425 311 152 27 25 2 102 60 131 155 324 241 t 0 0 677 1953 223 3062 67 18 108 3067 97 2713 713 1956
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --atATACATATat ; cor=; Ncor= a 0 0 1975 662 2891 99 3220 1 3115 75 3109 241 2130 728 c 0 0 295 446 106 184 60 3351 47 170 35 263 205 447 g 0 0 425 311 152 27 25 2 102 60 131 155 324 241 t 0 0 677 1953 223 3062 67 18 108 3067 97 2713 713 1956
positions_7nt_m1_shift3 (positions_7nt_m1)				; oligos_6nt_mkv3_m1 versus positions_7nt_m1; m=2/3; ncol2=12; w=0; offset=1; strand=D; shift=3; score=0.68017; ---taTATATATAt ; cor=; Ncor= a 0 0 0 555 2104 6 3295 6 3303 1 3301 2 3303 376 c 0 0 0 619 238 8 14 20 0 24 1 17 11 610 g 0 0 0 428 610 11 17 1 24 0 20 14 8 238 t 0 0 0 1726 376 3303 2 3301 1 3303 6 3295 6 2104
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m1 versus oligos_6nt_mkv3_m3; m=3/3; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.602031; atAGATAGATAdaw ; cor=; Ncor= a 1274 470 1437 63 1872 57 1881 46 1901 90 1670 725 1191 510 c 108 155 50 16 14 31 10 48 16 50 23 120 214 170 g 257 237 114 1754 44 61 37 1710 29 127 166 601 155 260 t 320 1097 358 126 29 1810 31 155 13 1692 100 513 399 1019

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m5_shift2 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=14; shift=2; ncol=16; --mATCGAATGGAATc ; Alignment reference a 0 0 1081 1478 78 60 249 1903 1906 39 45 61 1932 1487 176 155 c 0 0 703 254 76 1445 35 21 15 31 29 85 8 197 104 1232 g 0 0 58 83 37 282 1637 22 37 12 1902 1806 13 38 60 339 t 0 0 158 185 1809 213 79 54 42 1918 24 48 47 278 1660 274
oligos_6nt_mkv3_m5_shift2 (oligos_6nt_mkv3_m5)				; oligos_6nt_mkv3_m5 versus oligos_6nt_mkv3_m5; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=2; score= 1; --mATCGAATGGAATc ; cor=; Ncor= a 0 0 1081 1478 78 60 249 1903 1906 39 45 61 1932 1487 176 155 c 0 0 703 254 76 1445 35 21 15 31 29 85 8 197 104 1232 g 0 0 58 83 37 282 1637 22 37 12 1902 1806 13 38 60 339 t 0 0 158 185 1809 213 79 54 42 1918 24 48 47 278 1660 274
oligos_7nt_mkv4_m1_rc_shift0 (oligos_7nt_mkv4_m1_rc)				; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m1_rc; m=2/3; ncol2=16; w=-2; offset=-2; strand=R; shift=0; score=0.869447; rkmATcGAATGGAATc ; cor=; Ncor= a 1052 275 1353 2061 102 127 330 2417 2437 49 106 81 2376 2163 202 229 c 312 114 977 260 88 1547 50 34 30 95 251 61 36 219 125 1404 g 1011 1184 51 98 40 567 2076 40 43 45 2129 2352 44 47 90 607 t 165 967 159 121 2310 299 84 49 30 2351 54 46 84 111 2123 300
oligos_7nt_mkv4_m4_rc_shift2 (oligos_7nt_mkv4_m4_rc)				; oligos_6nt_mkv3_m5 versus oligos_7nt_mkv4_m4_rc; m=3/3; ncol2=12; w=0; offset=0; strand=R; shift=2; score=0.623518; --AATGGAATCrwm-- ; cor=; Ncor= a 0 0 1589 1592 31 50 42 1844 1654 61 44 654 1110 1032 0 0 c 0 0 118 60 75 7 50 24 172 40 1513 39 83 568 0 0 g 0 0 93 128 17 1833 1795 17 19 16 284 1171 94 111 0 0 t 0 0 124 144 1801 34 37 39 79 1807 83 60 637 213 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; atAGATAGATAdaw ; Alignment reference a 1274 470 1437 63 1872 57 1881 46 1901 90 1670 725 1191 510 c 108 155 50 16 14 31 10 48 16 50 23 120 214 170 g 257 237 114 1754 44 61 37 1710 29 127 166 601 155 260 t 320 1097 358 126 29 1810 31 155 13 1692 100 513 399 1019
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m3; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score= 1; atAGATAGATAdaw ; cor=; Ncor= a 1274 470 1437 63 1872 57 1881 46 1901 90 1670 725 1191 510 c 108 155 50 16 14 31 10 48 16 50 23 120 214 170 g 257 237 114 1754 44 61 37 1710 29 127 166 601 155 260 t 320 1097 358 126 29 1810 31 155 13 1692 100 513 399 1019
oligos_7nt_mkv4_m2_rc_shift1 (oligos_7nt_mkv4_m2_rc)				; oligos_6nt_mkv3_m3 versus oligos_7nt_mkv4_m2_rc; m=2/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.778447; -wAGATAGATAd-- ; cor=; Ncor= a 0 471 1204 0 1587 74 1675 4 1621 118 1235 482 0 0 c 0 113 45 0 27 32 5 2 26 61 61 145 0 0 g 0 218 81 1753 60 80 32 1731 48 104 200 607 0 0 t 0 952 424 1 80 1568 42 17 59 1471 258 520 0 0
oligos_6nt_mkv3_m1_shift2 (oligos_6nt_mkv3_m1)				; oligos_6nt_mkv3_m3 versus oligos_6nt_mkv3_m1; m=3/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.602031; --atATACATATat ; cor=; Ncor= a 0 0 1975 662 2891 99 3220 1 3115 75 3109 241 2130 728 c 0 0 295 446 106 184 60 3351 47 170 35 263 205 447 g 0 0 425 311 152 27 25 2 102 60 131 155 324 241 t 0 0 677 1953 223 3062 67 18 108 3067 97 2713 713 1956

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; waAAGAAAAAAww ; Alignment reference a 825 874 1595 1673 1 1678 1652 1638 1616 1578 1593 826 803 c 194 199 67 7 1 37 44 43 42 69 55 177 188 g 341 310 82 70 1804 52 77 83 84 58 61 297 277 t 474 451 90 84 28 67 61 70 92 129 125 534 566
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)				; oligos_7nt_mkv4_m3 versus oligos_7nt_mkv4_m3; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score= 1; waAAGAAAAAAww ; cor=; Ncor= a 825 874 1595 1673 1 1678 1652 1638 1616 1578 1593 826 803 c 194 199 67 7 1 37 44 43 42 69 55 177 188 g 341 310 82 70 1804 52 77 83 84 58 61 297 277 t 474 451 90 84 28 67 61 70 92 129 125 534 566
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; oligos_7nt_mkv4_m3 versus oligos_6nt_mkv3_m4; m=2/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score=0.71533; wwAAGAAAAcAAA ; cor=; Ncor= a 473 473 733 922 44 905 939 909 937 165 902 807 848 c 111 116 80 10 37 18 19 34 10 646 32 43 28 g 163 153 77 25 895 35 26 33 25 57 31 67 53 t 271 276 128 61 42 60 34 42 46 150 53 101 89
positions_6nt_m5_shift1 (positions_6nt_m5)				; oligos_7nt_mkv4_m3 versus positions_6nt_m5; m=3/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.703898; -wwAGAAAAww-- ; cor=; Ncor= a 0 1054 965 2287 0 2288 2287 2287 2287 967 1043 0 0 c 0 231 346 1 0 0 0 0 1 301 273 0 0 g 0 375 384 0 2288 0 0 0 0 321 328 0 0 t 0 628 593 0 0 0 1 1 0 699 644 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift5 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=14; shift=5; ncol=19; -----wwTTAAAAATAAww ; Alignment reference a 0 0 0 0 0 471 412 93 70 1057 1103 1135 1127 1104 68 1067 1029 516 466 c 0 0 0 0 0 133 149 26 34 36 12 14 19 21 27 28 45 152 151 g 0 0 0 0 0 153 132 33 28 29 37 12 8 25 36 25 16 147 157 t 0 0 0 0 0 435 499 1040 1060 70 40 31 38 42 1061 72 102 377 418
positions_6nt_m3_shift5 (positions_6nt_m3)				; positions_6nt_m3 versus positions_6nt_m3; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=5; score= 1; -----wwTTAAAAATAAww ; cor=; Ncor= a 0 0 0 0 0 471 412 93 70 1057 1103 1135 1127 1104 68 1067 1029 516 466 c 0 0 0 0 0 133 149 26 34 36 12 14 19 21 27 28 45 152 151 g 0 0 0 0 0 153 132 33 28 29 37 12 8 25 36 25 16 147 157 t 0 0 0 0 0 435 499 1040 1060 70 40 31 38 42 1061 72 102 377 418
positions_6nt_m1_shift5 (positions_6nt_m1)				; positions_6nt_m3 versus positions_6nt_m1; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=5; score=0.891315; -----wwTTAAAAATATww ; cor=; Ncor= a 0 0 0 0 0 403 352 60 47 995 1045 1080 1069 1059 59 1024 74 428 386 c 0 0 0 0 0 138 143 17 27 41 18 19 14 19 24 23 42 121 136 g 0 0 0 0 0 133 124 22 30 28 32 14 11 18 19 37 16 180 117 t 0 0 0 0 0 476 531 1051 1046 86 55 37 56 54 1048 66 1018 421 511
positions_6nt_m2_shift4 (positions_6nt_m2)				; positions_6nt_m3 versus positions_6nt_m2; m=3/4; ncol2=15; w=-1; offset=-1; strand=D; shift=4; score=0.719522; ----wwTTAAAAAATATww ; cor=; Ncor= a 0 0 0 0 186 170 15 3 410 440 457 456 421 445 18 448 38 184 148 c 0 0 0 0 68 51 6 8 11 9 4 4 5 9 11 9 21 43 51 g 0 0 0 0 44 55 4 18 13 11 11 8 10 8 3 15 10 75 51 t 0 0 0 0 190 212 463 459 54 28 16 20 52 26 456 16 419 186 238
oligos_6nt_mkv3_m2_rc_shift0 (oligos_6nt_mkv3_m2_rc)				; positions_6nt_m3 versus oligos_6nt_mkv3_m2_rc; m=4/4; ncol2=20; w=-5; offset=-5; strand=R; shift=0; score=0.584975; wwTTTATTTTAAAATAAAw ; cor=; Ncor= a 130 123 55 43 37 281 20 37 34 35 275 290 281 294 24 280 272 242 127 c 29 33 25 6 9 13 9 9 6 20 7 5 7 12 18 10 16 14 53 g 35 54 14 16 10 18 12 7 5 7 20 7 10 9 13 9 6 25 33 t 142 126 242 271 280 24 295 283 291 274 34 34 38 21 281 37 42 55 123

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift5 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=14; shift=5; ncol=19; -----wwTTAAAAATATww ; Alignment reference a 0 0 0 0 0 403 352 60 47 995 1045 1080 1069 1059 59 1024 74 428 386 c 0 0 0 0 0 138 143 17 27 41 18 19 14 19 24 23 42 121 136 g 0 0 0 0 0 133 124 22 30 28 32 14 11 18 19 37 16 180 117 t 0 0 0 0 0 476 531 1051 1046 86 55 37 56 54 1048 66 1018 421 511
positions_6nt_m1_shift5 (positions_6nt_m1)				; positions_6nt_m1 versus positions_6nt_m1; m=1/4; ncol2=14; w=0; offset=0; strand=D; shift=5; score= 1; -----wwTTAAAAATATww ; cor=; Ncor= a 0 0 0 0 0 403 352 60 47 995 1045 1080 1069 1059 59 1024 74 428 386 c 0 0 0 0 0 138 143 17 27 41 18 19 14 19 24 23 42 121 136 g 0 0 0 0 0 133 124 22 30 28 32 14 11 18 19 37 16 180 117 t 0 0 0 0 0 476 531 1051 1046 86 55 37 56 54 1048 66 1018 421 511
positions_6nt_m3_shift5 (positions_6nt_m3)				; positions_6nt_m1 versus positions_6nt_m3; m=2/4; ncol2=14; w=0; offset=0; strand=D; shift=5; score=0.891315; -----wwTTAAAAATAAww ; cor=; Ncor= a 0 0 0 0 0 471 412 93 70 1057 1103 1135 1127 1104 68 1067 1029 516 466 c 0 0 0 0 0 133 149 26 34 36 12 14 19 21 27 28 45 152 151 g 0 0 0 0 0 153 132 33 28 29 37 12 8 25 36 25 16 147 157 t 0 0 0 0 0 435 499 1040 1060 70 40 31 38 42 1061 72 102 377 418
positions_6nt_m2_shift4 (positions_6nt_m2)				; positions_6nt_m1 versus positions_6nt_m2; m=3/4; ncol2=15; w=-1; offset=-1; strand=D; shift=4; score=0.814132; ----wwTTAAAAAATATww ; cor=; Ncor= a 0 0 0 0 186 170 15 3 410 440 457 456 421 445 18 448 38 184 148 c 0 0 0 0 68 51 6 8 11 9 4 4 5 9 11 9 21 43 51 g 0 0 0 0 44 55 4 18 13 11 11 8 10 8 3 15 10 75 51 t 0 0 0 0 190 212 463 459 54 28 16 20 52 26 456 16 419 186 238
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; positions_6nt_m1 versus oligos_6nt_mkv3_m2; m=4/4; ncol2=20; w=-5; offset=-5; strand=D; shift=0; score=0.519475; wwTTTATTTTAAAATAAAw ; cor=; Ncor= a 130 123 55 42 37 281 21 38 34 34 274 291 283 295 24 280 271 242 126 c 29 33 25 6 9 13 9 10 7 20 7 5 7 12 18 10 16 14 54 g 34 53 14 16 10 18 12 7 5 7 20 6 9 9 13 9 6 25 33 t 143 127 242 272 280 24 294 281 290 275 35 34 37 20 281 37 43 55 123

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; wwAAGAAAAcAAAaww ; Alignment reference a 473 473 733 922 44 905 939 909 937 165 902 807 848 639 455 456 c 111 116 80 10 37 18 19 34 10 646 32 43 28 73 112 130 g 163 153 77 25 895 35 26 33 25 57 31 67 53 91 152 128 t 271 276 128 61 42 60 34 42 46 150 53 101 89 215 299 304
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; oligos_6nt_mkv3_m4 versus oligos_6nt_mkv3_m4; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=0; score= 1; wwAAGAAAAcAAAaww ; cor=; Ncor= a 473 473 733 922 44 905 939 909 937 165 902 807 848 639 455 456 c 111 116 80 10 37 18 19 34 10 646 32 43 28 73 112 130 g 163 153 77 25 895 35 26 33 25 57 31 67 53 91 152 128 t 271 276 128 61 42 60 34 42 46 150 53 101 89 215 299 304
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)				; oligos_6nt_mkv3_m4 versus oligos_7nt_mkv4_m3; m=2/3; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.71533; waAAGAAAAAAww--- ; cor=; Ncor= a 825 874 1595 1673 1 1678 1652 1638 1616 1578 1593 826 803 0 0 0 c 194 199 67 7 1 37 44 43 42 69 55 177 188 0 0 0 g 341 310 82 70 1804 52 77 83 84 58 61 297 277 0 0 0 t 474 451 90 84 28 67 61 70 92 129 125 534 566 0 0 0
positions_6nt_m5_shift1 (positions_6nt_m5)				; oligos_6nt_mkv3_m4 versus positions_6nt_m5; m=3/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.570247; -wwAGAAAAww----- ; cor=; Ncor= a 0 1054 965 2287 0 2288 2287 2287 2287 967 1043 0 0 0 0 0 c 0 231 346 1 0 0 0 0 1 301 273 0 0 0 0 0 g 0 375 384 0 2288 0 0 0 0 321 328 0 0 0 0 0 t 0 628 593 0 0 0 1 1 0 699 644 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --kwyGATTCCATT ; Alignment reference a 0 0 213 637 60 83 1807 79 39 37 34 1801 144 124 c 0 0 111 94 1171 284 16 19 17 1795 1833 17 128 93 g 0 0 568 83 39 1513 40 172 24 50 7 75 60 118 t 0 0 1032 1110 654 44 61 1654 1844 42 50 31 1592 1589
oligos_7nt_mkv4_m4_shift2 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m4; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score= 1; --kwyGATTCCATT ; cor=; Ncor= a 0 0 213 637 60 83 1807 79 39 37 34 1801 144 124 c 0 0 111 94 1171 284 16 19 17 1795 1833 17 128 93 g 0 0 568 83 39 1513 40 172 24 50 7 75 60 118 t 0 0 1032 1110 654 44 61 1654 1844 42 50 31 1592 1589
oligos_6nt_mkv3_m5_rc_shift0 (oligos_6nt_mkv3_m5_rc)				; oligos_7nt_mkv4_m4 versus oligos_6nt_mkv3_m5_rc; m=2/3; ncol2=14; w=-2; offset=-2; strand=R; shift=0; score=0.623518; gATTCCATTCGATk ; cor=; Ncor= a 274 1660 278 47 48 24 1918 42 54 79 213 1809 185 158 c 339 60 38 13 1806 1902 12 37 22 1637 282 37 83 58 g 1232 104 197 8 85 29 31 15 21 35 1445 76 254 703 t 155 176 1487 1932 61 45 39 1906 1903 249 60 78 1478 1081
oligos_7nt_mkv4_m1_shift0 (oligos_7nt_mkv4_m1)				; oligos_7nt_mkv4_m4 versus oligos_7nt_mkv4_m1; m=3/3; ncol2=16; w=-2; offset=-2; strand=D; shift=0; score=0.576402; gATTCCATTCgATk ; cor=; Ncor= a 300 2123 111 84 46 54 2351 30 49 84 299 2310 121 159 c 607 90 47 44 2352 2129 45 43 40 2076 567 40 98 51 g 1404 125 219 36 61 251 95 30 34 50 1547 88 260 977 t 229 202 2163 2376 81 106 49 2437 2417 330 127 102 2061 1353

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; wwTTTATTTTAAAATAAAww ; Alignment reference a 130 123 55 42 37 281 21 38 34 34 274 291 283 295 24 280 271 242 126 142 c 29 33 25 6 9 13 9 10 7 20 7 5 7 12 18 10 16 14 54 35 g 34 53 14 16 10 18 12 7 5 7 20 6 9 9 13 9 6 25 33 29 t 143 127 242 272 280 24 294 281 290 275 35 34 37 20 281 37 43 55 123 130
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2 versus oligos_6nt_mkv3_m2; m=1/4; ncol2=20; w=0; offset=0; strand=D; shift=0; score= 1; wwTTTATTTTAAAATAAAww ; cor=; Ncor= a 130 123 55 42 37 281 21 38 34 34 274 291 283 295 24 280 271 242 126 142 c 29 33 25 6 9 13 9 10 7 20 7 5 7 12 18 10 16 14 54 35 g 34 53 14 16 10 18 12 7 5 7 20 6 9 9 13 9 6 25 33 29 t 143 127 242 272 280 24 294 281 290 275 35 34 37 20 281 37 43 55 123 130
positions_6nt_m3_rc_shift1 (positions_6nt_m3_rc)				; oligos_6nt_mkv3_m2 versus positions_6nt_m3_rc; m=2/4; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.584975; -wwTTATTTTTAAww----- ; cor=; Ncor= a 0 418 377 102 72 1061 42 38 31 40 70 1060 1040 499 435 0 0 0 0 0 c 0 157 147 16 25 36 25 8 12 37 29 28 33 132 153 0 0 0 0 0 g 0 151 152 45 28 27 21 19 14 12 36 34 26 149 133 0 0 0 0 0 t 0 466 516 1029 1067 68 1104 1127 1135 1103 1057 70 93 412 471 0 0 0 0 0
positions_6nt_m1_shift5 (positions_6nt_m1)				; oligos_6nt_mkv3_m2 versus positions_6nt_m1; m=3/4; ncol2=14; w=0; offset=5; strand=D; shift=5; score=0.519475; -----wwTTAAAAATATww- ; cor=; Ncor= a 0 0 0 0 0 403 352 60 47 995 1045 1080 1069 1059 59 1024 74 428 386 0 c 0 0 0 0 0 138 143 17 27 41 18 19 14 19 24 23 42 121 136 0 g 0 0 0 0 0 133 124 22 30 28 32 14 11 18 19 37 16 180 117 0 t 0 0 0 0 0 476 531 1051 1046 86 55 37 56 54 1048 66 1018 421 511 0
positions_6nt_m2_shift6 (positions_6nt_m2)				; oligos_6nt_mkv3_m2 versus positions_6nt_m2; m=4/4; ncol2=15; w=0; offset=6; strand=D; shift=6; score=0.47922; ------wwTTAAAAAATATw ; cor=; Ncor= a 0 0 0 0 0 0 186 170 15 3 410 440 457 456 421 445 18 448 38 184 c 0 0 0 0 0 0 68 51 6 8 11 9 4 4 5 9 11 9 21 43 g 0 0 0 0 0 0 44 55 4 18 13 11 11 8 10 8 3 15 10 75 t 0 0 0 0 0 0 190 212 463 459 54 28 16 20 52 26 456 16 419 186

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m5_shift1 (positions_6nt_m5)				; positions_6nt_m5; m=0 (reference); ncol1=10; shift=1; ncol=11; -wwAGAAAAww ; Alignment reference a 0 1054 965 2287 0 2288 2287 2287 2287 967 1043 c 0 231 346 1 0 0 0 0 1 301 273 g 0 375 384 0 2288 0 0 0 0 321 328 t 0 628 593 0 0 0 1 1 0 699 644
positions_6nt_m5_shift1 (positions_6nt_m5)				; positions_6nt_m5 versus positions_6nt_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 1; -wwAGAAAAww ; cor=; Ncor= a 0 1054 965 2287 0 2288 2287 2287 2287 967 1043 c 0 231 346 1 0 0 0 0 1 301 273 g 0 375 384 0 2288 0 0 0 0 321 328 t 0 628 593 0 0 0 1 1 0 699 644
oligos_7nt_mkv4_m3_shift0 (oligos_7nt_mkv4_m3)				; positions_6nt_m5 versus oligos_7nt_mkv4_m3; m=2/3; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.703898; waAAGAAAAAA ; cor=; Ncor= a 825 874 1595 1673 1 1678 1652 1638 1616 1578 1593 c 194 199 67 7 1 37 44 43 42 69 55 g 341 310 82 70 1804 52 77 83 84 58 61 t 474 451 90 84 28 67 61 70 92 129 125
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)				; positions_6nt_m5 versus oligos_6nt_mkv3_m4; m=3/3; ncol2=16; w=-1; offset=-1; strand=D; shift=0; score=0.570247; wwAAGAAAAcA ; cor=; Ncor= a 473 473 733 922 44 905 939 909 937 165 902 c 111 116 80 10 37 18 19 34 10 646 32 g 163 153 77 25 895 35 26 33 25 57 31 t 271 276 128 61 42 60 34 42 46 150 53

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift6 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=15; shift=6; ncol=21; ------wwTTAAAAAATATww ; Alignment reference a 0 0 0 0 0 0 186 170 15 3 410 440 457 456 421 445 18 448 38 184 148 c 0 0 0 0 0 0 68 51 6 8 11 9 4 4 5 9 11 9 21 43 51 g 0 0 0 0 0 0 44 55 4 18 13 11 11 8 10 8 3 15 10 75 51 t 0 0 0 0 0 0 190 212 463 459 54 28 16 20 52 26 456 16 419 186 238
positions_6nt_m2_shift6 (positions_6nt_m2)				; positions_6nt_m2 versus positions_6nt_m2; m=1/5; ncol2=15; w=0; offset=0; strand=D; shift=6; score= 1; ------wwTTAAAAAATATww ; cor=; Ncor= a 0 0 0 0 0 0 186 170 15 3 410 440 457 456 421 445 18 448 38 184 148 c 0 0 0 0 0 0 68 51 6 8 11 9 4 4 5 9 11 9 21 43 51 g 0 0 0 0 0 0 44 55 4 18 13 11 11 8 10 8 3 15 10 75 51 t 0 0 0 0 0 0 190 212 463 459 54 28 16 20 52 26 456 16 419 186 238
positions_6nt_m1_shift7 (positions_6nt_m1)				; positions_6nt_m2 versus positions_6nt_m1; m=2/5; ncol2=14; w=0; offset=1; strand=D; shift=7; score=0.814132; -------wwTTAAAAATATww ; cor=; Ncor= a 0 0 0 0 0 0 0 403 352 60 47 995 1045 1080 1069 1059 59 1024 74 428 386 c 0 0 0 0 0 0 0 138 143 17 27 41 18 19 14 19 24 23 42 121 136 g 0 0 0 0 0 0 0 133 124 22 30 28 32 14 11 18 19 37 16 180 117 t 0 0 0 0 0 0 0 476 531 1051 1046 86 55 37 56 54 1048 66 1018 421 511
positions_6nt_m3_shift7 (positions_6nt_m3)				; positions_6nt_m2 versus positions_6nt_m3; m=3/5; ncol2=14; w=0; offset=1; strand=D; shift=7; score=0.719522; -------wwTTAAAAATAAww ; cor=; Ncor= a 0 0 0 0 0 0 0 471 412 93 70 1057 1103 1135 1127 1104 68 1067 1029 516 466 c 0 0 0 0 0 0 0 133 149 26 34 36 12 14 19 21 27 28 45 152 151 g 0 0 0 0 0 0 0 153 132 33 28 29 37 12 8 25 36 25 16 147 157 t 0 0 0 0 0 0 0 435 499 1040 1060 70 40 31 38 42 1061 72 102 377 418
oligos_6nt_mkv3_m2_shift0 (oligos_6nt_mkv3_m2)				; positions_6nt_m2 versus oligos_6nt_mkv3_m2; m=4/5; ncol2=20; w=-6; offset=-6; strand=D; shift=0; score=0.47922; wwTTTATTTTAAAATAAAww- ; cor=; Ncor= a 130 123 55 42 37 281 21 38 34 34 274 291 283 295 24 280 271 242 126 142 0 c 29 33 25 6 9 13 9 10 7 20 7 5 7 12 18 10 16 14 54 35 0 g 34 53 14 16 10 18 12 7 5 7 20 6 9 9 13 9 6 25 33 29 0 t 143 127 242 272 280 24 294 281 290 275 35 34 37 20 281 37 43 55 123 130 0
positions_6nt_m4_rc_shift6 (positions_6nt_m4_rc)				; positions_6nt_m2 versus positions_6nt_m4_rc; m=5/5; ncol2=10; w=0; offset=0; strand=R; shift=6; score=0.478914; ------wwTTAATAww----- ; cor=; Ncor= a 0 0 0 0 0 0 595 740 0 0 1871 1871 0 1871 599 727 0 0 0 0 0 c 0 0 0 0 0 0 245 197 0 0 0 0 0 0 230 241 0 0 0 0 0 g 0 0 0 0 0 0 216 222 0 0 0 0 0 0 224 262 0 0 0 0 0 t 0 0 0 0 0 0 815 712 1871 1871 0 0 1871 0 818 641 0 0 0 0 0