Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1pyya1
CCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEECCCCCEEEECCCCCCCCCCCCEEEEEECC

>P1;d1pyya2
---CCCCCCCCCCCHHHHHHHHHHCCCEEEEECCCCEEEEECCCCCCCHHHCCEEEEEEEC
PSA

>P1;d1pyya1
a797260243792409600630663806053559198078150968660527470504048

>P1;d1pyya2
---8950270663548504421872b070516a9192028161929351a72a40203039


Translating the sequences
***CCCCCCCCCCCHHHHHHHHHHCCCEEEEECCCC*EEEECCCCCCC***CCEEEEEE*C
---CCCCCCCCCCCHHHHHHHHHHCCCEEEEECCCCEEEEECCCCCCCHHHCCEEEEEEEC

54184.tem
_________________________________
---CCCCCCCCCCCHHHHHHHHHHCCCEEEEECCCCEEEEECCCCCCCHHHCCEEEEEEEC




Structural block scores
0	2	-	3.0	P	  8.8  75.0

3	13	C	5.0	H	  4.2  4.6

14	23	H	5.0	H	  3.6  4.3

24	26	C	5.0	H	  3.7  4.5

27	31	E	5.0	H	  3.8  3.8

32	35	C	5.0	H	  6.0  7.4

36	40	E	4.6	H	  4.8  2.6

41	47	C	5.0	H	  5.7  5.0

48	50	H	3.0	P	  2.3  6.2

51	52	C	5.0	H	  5.5  6.2

53	59	E	4.7	H	  2.9  1.7

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