[Gramene] Help regarding BLAST result summary

[Mauro-Herrera, Margarita]

Hello,
  My name is Margarita Mauro and I have been doing some BLAST searches using Gramene. It is working fine with the exception that there is a step that is taking a loong time when I do my alignments with the sequences/hits from my BLAST searches. That is putting all the hits/sequences in the same orientation so I can do my alignments with MAFFT (the alignment program that requires all the sequences to be in the same orientation). I wonder if there is a way to get the orientation of the sequences/hits as another column in the BLAST result summary table (where you get the hit ID, the BLAST score and the BLAST E-value)? Or if the information regarding the direction of the hit sequences with respect to the query can be downloaded somehow when you display the hits as FASTA files?

Please, let me know if you understand my questions and if there is anything that can be done to help me out.
Thanks in advance and I look forward to hearing from you,
Margarita