Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2c9wa1
CCCCCCCCCCCCCHHHHHHHHHHHHCC--CHHHCCCCHHHHHHHHCCCC-C

>P1;d2izva1
----------CCCHHHHHHHHHHHHCCHHHHHCCCCCHHHHHHHCCCCCCC
PSA

>P1;d2c9wa1
b89775a4b99278724610731573b--41882934873272077387-7

>P1;d2izva1
----------b879525605743a7295a6069283788429202675a7b


Translating the sequences
**********CCCHHHHHHHHHHHHCC--*HHHCCCCHHHHHHHHCCCC-C
----------CCCHHHHHHHHHHHHCC**HHH*CCCCHHHHHHH*CCCC*C

158235.tem
_________________________________
----------CCCHHHHHHHHHHHHCC--HHHHCCCCHHHHHHHHCCCC-C




Structural block scores
0	9	-	3.0	P	  8.2  75.0

10	12	C	5.0	H	  6.0  8.8

13	24	H	5.0	H	  4.2  5.3

25	26	C	5.0	H	  7.2  5.5

27	28	-	3.0	P	  75.0  7.8

29	32	H	4.0	M	  5.2  5.2

33	36	C	5.0	H	  4.5  5.0

37	44	H	4.8	H	  4.5  4.4

45	48	C	5.0	H	  6.2  7.1

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