Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1f5na1
CCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC

>P1;d6vkja2
CCCCCCHHHHHHHHHHHHHHHHCCCCCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
PSA

>P1;d1f5na1
592a4796268126723672776a7a3487603440077206700760063046108640721065053006203400330041016301417746207503730563146217505730483069118800260163166550485410770274045127503637300111242017226725a11670054065078850682474177347833751672674385127608761751158016724676663647416742753576286269776775076158507715871

>P1;d6vkja2
bb8838a65675577777876775998a--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------


Translating the sequences
CCCCCCHHHHHHHHHHHHHHHHHCCCCC********************************************************************************************************************************************************************************************************************************************************************************
CCCCCCHHHHHHHHHHHHHHHH*CCCCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

48340.tem
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CCCCCCHHHHHHHHHHHHHHHHHCCCCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------




Structural block scores
0	5	C	5.0	H	  6.2  8.3

6	22	H	4.9	H	  5.1  6.7

23	27	C	5.0	H	  7.0  8.3

28	299	-	3.0	P	  3.9  75.0

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