Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1h9ea-
C-CCCCCCC--CCCCCHHHHHHHHHCCC-CCCCCCCCCHHHHHHHHHCCCCCCCCCCCCC

>P1;d1h9fa-
CCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHH-CCCCCCC--CC
PSA

>P1;d1h9ea-
9-8011709--91636301830762c1b-231b9368420381057307037559759ab

>P1;d1h9fa-
7b7532756038088980491075391a0a7087a1276115501760-2467697--ae


Translating the sequences
C-CCCCCCC--CCC**HHHHHHHHHCCC-CCCCCC***HHHHHHHHH**CCCCCCC**CC
C*CCCCCCC**CCCHHHHHHHHHHHCCC*CCCCCCHHHHHHHHHHHHH-CCCCCCC--CC

63451.tem
_________________________________
C-CCCCCCC--CCCHHHHHHHHHHHCCC-CCCCCCHHHHHHHHHHHHH-CCCCCCC--CC




Structural block scores
2	8	C	5.0	H	  3.7  5.0

9	10	-	3.0	P	  75.0  1.5

11	13	C	5.0	H	  5.3  5.3

14	24	H	4.6	H	  3.5  4.9

25	27	C	5.0	H	  8.3  6.8

29	34	C	5.0	H	  4.9  7.2

35	47	H	4.4	M	  3.6  3.2

49	55	C	5.0	H	  5.1  5.9

56	57	-	3.0	P	  7.0  75.0

58	59	C	5.0	H	  11.0  12.5

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