dnadiff in repeat ?

[Lcornet]

Dear mummer team,

I try to map a BAC of a repeat region on an ONT assembly with nucmer and dandify :

nucmer --prefix=55D23 60444-bacs.fasta hybrid.fasta
dnadiff -p 55D23 -d 55D23.delta

This bac fully map on the genome with mismatchs :
Mes-B-60444-55D23 Super-Scaffold_100051 96.12 80300 657 1827 1 78430 2659841 2739549 0.0 1.177e+05

The result of dnadiff is :
[REF] [QRY]
[Sequences]
TotalSeqs 1 131
AlignedSeqs 1(100.00%) 128(97.71%)
UnalignedSeqs 0(0.00%) 3(2.29%)

[Bases]
TotalBases 78430 1212883466
AlignedBases 78430(100.00%) 55347196(4.56%)
UnalignedBases 0(0.00%) 1157536270(95.44%)

[Alignments]
1-to-1 1 1
TotalLength 78430 79709
AvgLength 78430.00 79709.00
AvgIdentity 96.12 96.12

M-to-M 72161 72161
TotalLength 55037428 55876038
AvgLength 762.70 774.32
AvgIdentity 84.43 84.43

[Feature Estimates]
Breakpoints 143945 144321
Relocations 0 0
Translocations 0 0
Inversions 0 0

Insertions 0 141841
InsertionSum 0 1210833319
InsertionAvg 0.00 8536.55

TandemIns 0 0
TandemInsSum 0 0
TandemInsAvg 0.00 0.00

It seems that the number of events are too high compare to the blast reports ? Is it due to the repetitive regions (misplacement of clusters ?) ? I don't understand why the number of breakpoints are higher than the BAC length.