; One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 4 matrices ; sort_field=rank_mean ; dyads_m1; m=0 (reference); ncol1=20; shift=0; ncol=20; wwwTTGATctadATCAAwww ; Alignment reference a 13 17 18 2 0 2 26 0 6 5 16 7 25 1 0 28 26 9 9 7 c 3 2 2 0 0 0 0 3 13 3 2 5 1 0 25 0 0 0 2 5 g 5 1 0 0 0 26 0 1 3 3 4 9 2 0 0 0 0 3 2 5 t 7 8 8 26 28 0 2 24 6 17 6 7 0 27 3 0 2 16 15 11 // ; dyads_m1 versus dyads_m2_rc; m=1/3; ncol2=20; w=20; offset=0; strand=R; shift=0; score= 1; wwaTTGATctasrTCAAwww ; cor=0.958; Ncor=0.958; logoDP=11.514; NIcor=0.947; NsEucl=0.972; SSD=0.615; NSW=0.985; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1 a 13 15 19 0 0 2 26 0 4 5 15 6 13 1 0 27 26 9 12 9 c 5 0 5 0 0 0 0 1 14 5 3 7 3 0 25 0 1 4 3 3 g 1 2 0 2 0 26 0 1 5 3 4 9 12 0 0 1 0 4 5 4 t 9 11 4 26 28 0 2 26 5 15 6 6 0 27 3 0 1 11 8 12 // ; dyads_m1 versus oligos_6nt_mkv2_rc; m=2/3; ncol2=11; w=11; offset=0; strand=R; shift=0; score= 3.5714; wyATTGATCta--------- ; cor=0.866; Ncor=0.477; logoDP=3.597; NIcor=0.103; NsEucl=0.923; SSD=1.422; NSW=0.935; rcor=3; rNcor=3; rlogoDP=5; rNIcor=5; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.571; match_rank=3 a 2 0 5 0 0 0 5 0 0 1 2 0 0 0 0 0 0 0 0 0 c 1 2 0 0 0 0 0 0 5 1 1 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 5 0 0 0 1 1 0 0 0 0 0 0 0 0 0 t 2 3 0 5 5 0 0 5 0 2 1 0 0 0 0 0 0 0 0 0 // ; dyads_m1 versus dyads_m3_rc; m=3/3; ncol2=11; w=11; offset=0; strand=R; shift=0; score= 4; waTTTGATCkr--------- ; cor=0.855; Ncor=0.470; logoDP=3.697; NIcor=0.126; NsEucl=0.919; SSD=1.575; NSW=0.928; rcor=4; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=4.000; match_rank=4 a 6 7 0 0 0 0 11 0 0 2 4 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0 g 1 2 0 0 0 11 0 0 0 3 3 0 0 0 0 0 0 0 0 0 t 4 2 11 11 11 0 0 11 0 6 2 0 0 0 0 0 0 0 0 0 // ; ; One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 3 matrices ; sort_field=rank_mean ; dyads_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; wwwTTGAystagATCAAtww ; Alignment reference a 12 8 11 1 0 3 27 0 6 6 15 5 26 2 0 28 26 4 11 9 c 4 5 4 0 1 0 0 12 9 4 3 5 1 0 26 0 2 0 2 1 g 3 3 4 1 0 25 0 3 7 3 5 14 1 0 0 0 0 5 0 5 t 9 12 9 26 27 0 1 13 6 15 5 4 0 26 2 0 0 19 15 13 // ; dyads_m2 versus oligos_6nt_mkv2; m=1/2; ncol2=11; w=11; offset=9; strand=D; shift=9; score= 2; ---------taGATCAATrw ; cor=0.900; Ncor=0.495; logoDP=8.396; NIcor=0.501; NsEucl=0.933; SSD=1.094; NSW=0.950; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2 a 0 0 0 0 0 0 0 0 0 1 2 0 5 0 0 5 5 0 3 2 c 0 0 0 0 0 0 0 0 0 1 1 0 0 0 5 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 1 1 5 0 0 0 0 0 0 2 1 t 0 0 0 0 0 0 0 0 0 2 1 0 0 5 0 0 0 5 0 2 // ; dyads_m2 versus dyads_m3; m=2/2; ncol2=11; w=11; offset=9; strand=D; shift=9; score= 4.4286; ---------ymGATCAAAtw ; cor=0.829; Ncor=0.456; logoDP=8.052; NIcor=0.449; NsEucl=0.913; SSD=1.822; NSW=0.917; rcor=5; rNcor=5; rlogoDP=3; rNIcor=3; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=4.429; match_rank=5 a 0 0 0 0 0 0 0 0 0 2 6 0 11 0 0 11 11 11 2 4 c 0 0 0 0 0 0 0 0 0 3 3 0 0 0 11 0 0 0 2 1 g 0 0 0 0 0 0 0 0 0 2 0 11 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 4 2 0 0 11 0 0 0 0 7 6 // ;