Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1pp9g-
---------CCCCCC--CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC---------

>P1;d3cx5h-
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHC
PSA

>P1;d1pp9g-
---------88ab84--8766867898657a65787566877755565766775588635676677786385585665667aa4---------

>P1;d3cx5h-
a899ba7b7478b84989a8ab76a99767a65879647a96568757796965368867565776787398565795166a8068226647b


Translating the sequences
---------CCCCCC--CCCCCCCCCCCC***CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH*CC***---------
*********CCCCCC**CCCCCCCCCCCCHHHCCCCCC**********HHHH**HHHHHHHHHHHHHHHHHHHHHHHHHCCHHH*********

81508.tem
_________________________________
---------CCCCCC--CCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH---------




Structural block scores
0	8	-	3.0	P	  75.0  9.3

9	14	C	5.0	H	  8.3  7.1

15	16	-	3.0	P	  75.0  8.5

17	28	C	5.0	H	  7.0  8.7

29	31	H	3.0	P	  7.8  7.8

32	37	C	5.0	H	  6.3  6.5

38	78	H	4.4	M	  6.1  6.5

79	80	C	5.0	H	  6.5  6.0

81	83	H	3.0	P	  8.3  6.2

84	92	-	3.0	P	  75.0  5.8

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