Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1k1va-
----------------CCHHHHHHCCHHHHCCCCC--CCCHHHHHHHHHHHHHHHHCCC---------------

>P1;d1sknp-
CCCCHHHHHHHHCCCCCCHHHHHHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
PSA

>P1;d1k1va-
----------------3877500816475069217--b25984387348717623a6d5---------------

>P1;d1sknp-
d965712530662903140860041778706723853b07962360065006325765646556757657979a


Translating the sequences
----------------CCHHHHHHCCHHHH*****--CCCHHHHHHHHHHHHHHHH***---------------
****************CCHHHHHHCCHHHHHHHHH**CCCHHHHHHHHHHHHHHHHHHH***************

47454.tem
_________________________________
----------------CCHHHHHHCCHHHHHHHHH--CCCHHHHHHHHHHHHHHHHHHH---------------




Structural block scores
0	15	-	3.0	P	  75.0  4.8

16	17	C	5.0	H	  5.5  2.5

18	23	H	5.0	H	  4.5  3.0

24	25	C	5.0	H	  3.5  4.0

26	34	H	3.9	M	  4.6  5.3

35	36	-	3.0	P	  75.0  4.0

37	39	C	5.0	H	  6.2  6.2

40	58	H	4.7	H	  6.1  4.1

59	73	-	3.0	P	  75.0  6.6

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