Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1rh5c-
CCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCC--------------------------------------

>P1;d3dine-
-----CHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCC
PSA

>P1;d1rh5c-
a7b69a7687876787666776656766859b--------------------------------------

>P1;d3dine-
-----9678634752751566476687b849664ca794b19878a88c7492674377277637744a9


Translating the sequences
*****C***HHHHHHHHHHHHHHHHHHHHCCC--------------------------------------
-----CHHHHHHHHHHHHHHHHHHHHH**CCC**************************************

267595.tem
_________________________________
-----CHHHHHHHHHHHHHHHHHHHHHHHCCC--------------------------------------




Structural block scores
0	4	-	3.0	P	  8.8  75.0

6	28	H	4.6	H	  6.7  5.9

29	31	C	5.0	H	  8.5  6.3

32	69	-	3.0	P	  75.0  6.8

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