Transcriptome Match in Colorspace

[doxologist]

I want to match to such a transcriptome file:

>TRANSCRIPT 1
AGTCACACAGTCACAGTCACACAGTCACAGTCACACAGTCACAGTCACACAGTCAC
>TRANSCRIPT 2
AGTCAACGTCACTGAGTCGTCAGTCAGTCGTAGTCACGTACGTAC
>TRANSCRIPT 3
ATCCATGCAGTCACAACGTCACTGAGTCGTCAGTCAGTCGTAGTCACGTACGTAC
etc

With the output being
G3112312312 TRANSCRIPT1 Pos23
G3123111231 TRANSCRIPT2 Pos43
etc

Coronoa Lite is genome centered and collapses each chromosome.
The Solid transcriptome pipeline seems also to be genome centered, just with specific file to delineate the exons.

Is there a simple way of doing this?

Thanks