Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1x3aa1
CCCHHHHHHHHHHHHHCHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHCCC

>P1;d2diia1
--------CCCCC----------------------CCHHHHHHHHHHHCHHHHHHHHHHCCCCCCCHHHHHHCCCCCC----------
PSA

>P1;d1x3aa1
78859505840281056470037606ad4b1d053992546056119408603511871087-12834300200103065256617b9

>P1;d2diia1
--------b97a8----------------------a5467515850a757924661263284c6385a6005c44cbe----------


Translating the sequences
********HHHHH**********************HHHHHHHHHHHHHCHHHHHHHHH*CCC-CCCHHHHHHHHHHHH**********
--------*****----------------------**HHHHHHHHHHHCHHHHHHHHHHCCC*CCCHHHHHH******----------

140383.tem
_________________________________
--------HHHHH----------------------HHHHHHHHHHHHHCHHHHHHHHHHCCC-CCCHHHHHHHHHHHH----------




Structural block scores
0	7	-	3.0	P	  5.9  75.0

8	12	H	3.0	P	  4.4  9.2

13	34	-	3.0	P	  4.9  75.0

35	47	H	4.7	H	  4.7  5.7

49	58	H	4.8	H	  4.0  4.6

59	61	C	5.0	H	  5.0  4.7

63	65	C	5.0	H	  3.7  5.7

66	77	H	4.0	M	  1.3  7.1

78	87	-	3.0	P	  5.8  75.0

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