Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1kbha-
-----CCCCCHHHHHHHHHHHCCCCCCCCHHHHHHCCCHHHHHHHCHHHCCC

>P1;d7jflc-
CCHHHCCCCCCHHHHHHHHHHHHH-CHHHHHHHHHHC---------------
PSA

>P1;d1kbha-
-----6998567855474597685b57b82467257785454887338a59a

>P1;d7jflc-
713862889057854674377077-468447645985---------------


Translating the sequences
-----CCCCCHHHHHHHHHHH****C***HHHHHH*C***************
*****CCCCC*HHHHHHHHHHHHH-CHHHHHHHHHHC---------------

69125.tem
_________________________________
-----CCCCCHHHHHHHHHHHHHH-CHHHHHHHHHHC---------------




Structural block scores
0	4	-	3.0	P	  75.0  5.0

5	9	C	5.0	H	  7.4  5.4

10	23	H	4.4	M	  6.1  5.5

26	35	H	4.2	M	  6.0  6.1

37	51	-	3.0	P	  6.5  75.0

>>>>>>