some problem of solexa results

[biocc]

hi, we sequencd two strain, one WT 36bp single end , mutated 76 single end.
and i usd AMOS to assemble them with a reference genome and vevlet do novo. what i find is some special congtigs form vlevet can not be aligned to the contigs by AMOS, neither in reference genome. what should i do next? thanks for any help.

[lmf_bill]

it seems to be some novel segments.