Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1ov9a-
---------------------CCHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH--------CC

>P1;d2l93a1
CCCCCCEEEECCCCEEEEECCC---------------------------CCCCHHHHHHHHHCCCCHHHCCCCC
PSA

>P1;d1ov9a-
---------------------a979348687436752772689537667875667666768668--------88

>P1;d2l93a1
b64904101777e75274162a---------------------------b9219506503679a4948512446


Translating the sequences
---------------------C***************************HHHHHHHHHHHHHHH--------CC
*********************C---------------------------****HHHHHHHHH**********CC

81273.tem
_________________________________
---------------------C---------------------------HHHHHHHHHHHHHHH--------CC




Structural block scores
0	20	-	3.0	P	  75.0  5.0

22	48	-	3.0	P	  6.0  75.0

49	63	H	4.2	M	  6.5  5.6

64	71	-	3.0	P	  75.0  4.6

72	73	C	5.0	H	  8.0  5.0

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