Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1tbge-
CCCCCCCCC-CHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCHHHHCCCHHHCCCC--

>P1;d3v5wg-
----CHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCHHHCCCCCCCCHHHCCCCCC
PSA

>P1;d1tbge-
9c4799557-766765795887a6589745656865756754ca46a7693598746a6--

>P1;d3v5wg-
----b88777776656686796b669a9656568877876439755a65726185359676


Translating the sequences
****C****-*HHHHHHHHHCCCCCCHHHHHHHHHHHHH*C***CHHHHCCCHHHCCCC--
----CHHHH*HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCHHHC****CCCHHHCCCC**

48670.tem
_________________________________
----CHHHH-HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCHHHCHHHHCCCHHHCCCC--




Structural block scores
0	3	-	3.0	P	  8.1  75.0

5	8	H	3.0	P	  6.5  7.5

10	19	H	4.8	H	  6.6  6.4

20	25	C	5.0	H	  7.4  7.9

26	39	H	4.9	H	  6.1  7.0

41	43	H	3.0	P	  9.0  6.3

45	48	H	3.0	P	  7.4  6.6

49	51	C	5.0	H	  5.7  5.0

52	54	H	5.0	H	  8.0  4.7

55	58	C	5.0	H	  6.6  5.8

59	60	-	3.0	P	  75.0  6.5

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