Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d5b5ee-
CCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCC

>P1;d5b5ef-
-----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC---------------CCC-----------------------
PSA

>P1;d5b5ee-
ea66985357398267437756568867876474626237579534893652a95a738474888393566368729

>P1;d5b5ef-
-----ba6774b9467647957468876a5578569---------------79b-----------------------


Translating the sequences
*****HHHCCCHHHHHHHHHHHHHHHHHHHHHHHCC***************CCC***********************
-----***CCCHHHHHHHHHHHHHHHHHHHHHHHCC---------------CCC-----------------------

161045.tem
_________________________________
-----HHHCCCHHHHHHHHHHHHHHHHHHHHHHHCC---------------CCC-----------------------




Structural block scores
0	4	-	3.0	P	  9.2  75.0

5	7	H	3.0	P	  5.3  9.3

8	10	C	5.0	H	  5.0  6.0

11	33	H	5.0	H	  6.1  6.7

34	35	C	5.0	H	  4.0  7.5

36	50	-	3.0	P	  5.5  75.0

51	53	C	5.0	H	  7.2  9.2

54	76	-	3.0	P	  6.1  75.0

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