Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1u96a-
CCCCCCCCCCCCCCCCCCCCCCCC-CCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC---------CCCCCCC---------C

>P1;d2hp8a-
--------------------CCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHHHCCCCC
PSA

>P1;d1u96a-
8a8a8778ab9c967794318359-417725772661377539948615635760467057b---------6180366---------d

>P1;d2hp8a-
--------------------784a03057204316612673865596058102600610384865106103a0273077279579b11


Translating the sequences
********************CCCC-CC*HHHHHHHHHHHHCCCC****HHHHHHHHHHHHCC---------*******---------C
--------------------CCCC*CCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH*CC*********HHHHHHH*********C

47072.tem
_________________________________
--------------------CCCC-CCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCC---------HHHHHHH---------C




Structural block scores
0	19	-	3.0	P	  7.8  75.0

20	23	C	5.0	H	  6.2  7.4

25	26	C	5.0	H	  2.5  1.5

27	39	H	4.8	H	  5.2  3.8

40	43	C	5.0	H	  6.5  5.5

44	59	H	4.4	M	  4.6  3.2

60	61	C	5.0	H	  9.2  6.0

62	70	-	3.0	P	  75.0  3.3

71	77	H	3.0	P	  4.3  4.2

78	86	-	3.0	P	  75.0  6.5

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