seqfile1_uc.out
>scaffold_2|GENSCAN_predicted_CDS_1|144_bp
atggatcggagtcatcagatatgggatgagaagctgatggatcagaagtgcgtcctctac
cccgtctgcctctggcacgagcaggagagcgagatgaactgggaggctgagaaagctgag
aggctaaggactgaacagaaaggn
>scaffold_2|GENSCAN_predicted_CDS_2|156_bp
atgaggaagaatgagggtgttgatgatgcagatccactaatagaaggtatgaaggagatc
actctgaaagattcagcaactccagaagacaaggatcaagaagacaaacaagatgagaga
ggtgaagaaattcaagaacaacctcaagagatgtag
........... so on... from all the 40,000 files.

seqfile2_uc.out
>scaffold_2|GENSCAN_predicted_peptide_1|48_aa
MDRSHQIWDEKLMDQKCVLYPVCLWHEQESEMNWEAEKAERLRTEQKX
>scaffold_2|GENSCAN_predicted_peptide_2|51_aa
MRKNEGVDDADPLIEGMKEITLKDSATPEDKDQEDKQDERGEEIQEQPQEM
....... so on...from all the 40,000 files.