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>input.fasta
GATCCccagagcgttGAwgcttAgacTCCgagc

 

#!/usr/bin/perl 
...
Command: pileup2markedfasta     generate maked.fasta from `pileup -c r
+aw pileup'
\n/);
}

2L    1    G    A    48    48    26    7    AAaaAAA    ACCCD?@
2L    2    A    A    48    0    26    7    ..,,...    AACC@BC
...
2L    32    g    G    90    0    37    21    .,..,,.,,.,,,,,,,,,,^F.  
+  CDCCCAC@@CDDCC<:DBABC
2L    33    c    C    117    0    14    31    ...,,*.,,-2gt.,,.,,.,...
+.......,,..    ;B6CCBBCBCACDCCCB@DCDCC8CCCABCC

>input.fasta
GATCCccagagcgttGAwgcttAgacTCCgagc
>input.fasta
AAKMMCYA----GNTGMTGCTTARWC----AGC