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I get a cDNA library of species of Mollusca,and complete some of the clones with polyA tails.But when I translate them with three frames,I find there is a large percentage of sequences that cannot make sense with a complete open reading frame.They have many Met and stop codons.I have checked sequencing results and assembly results. I wonder if these clones are chimeric clones.But the percentage of them is too much higher than I supposed.

Thanks in advance.

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put on hold as off-topic by Chris, MattDMo, WYSIWYG, GriffinEvo, Cornelius Dec 17 at 20:17

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You say that you have looked at three frames. Which end of the cDNA are you sequencing from - are you sure that you are translating the correct strand? –  Alan Boyd Jun 12 at 12:48
    
Sequencing is from the 5' end,and some of them have been sequenced to the polyA end.We all know that most mRNA's sequences end with a polyA end. –  shorebean Jun 13 at 1:29
    
ok, just thought that it was worth checking for a trivial explanation first! –  Alan Boyd Jun 13 at 18:21
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This question is most like impossible to answer, since we lack details. –  Chris Dec 17 at 16:26