Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d4cz5a-
CCCCCCCCCHHHHHHHHHHHHHHHHCCCC-------------

>P1;d5hobg-
CCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
PSA

>P1;d4cz5a-
b9988919a8765364476766879788e-------------

>P1;d5hobg-
97897b299987565447656677569467772677687586


Translating the sequences
CCCCCCCCCHHHHHHHHHHHHHHHHCCCC-------------
CCCCCCCCCHHHHHHHHHHHHHHHHCCCC*************

47719.tem
_________________________________
CCCCCCCCCHHHHHHHHHHHHHHHHCCCC-------------




Structural block scores
0	8	C	5.0	H	  8.3  7.9

9	24	H	5.0	H	  6.2  6.1

25	28	C	5.0	H	  9.4  6.2

29	41	-	3.0	P	  75.0  6.4

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