Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2pspa2
---CCHHHCCCHHHCCCCCCCCCCHHHHHHCCCEECCCCCCCCCEECCCCHHHCCC

>P1;d6v1ca-
CCCCCHHHCCCC-CCCCCCCCCCCC-CCHHHCCEECCCCCCCCCEECCCC-----C
PSA

>P1;d2pspa2
---7574081a49406700599045850785c00134848a12500525649959c

>P1;d6v1ca-
bc27ac328072-80a52058a085-309b4800234737c33400168b-----b


Translating the sequences
---CCHHHCCCH*HCCCCCCCCCCH*HHHH*CCEECCCCCCCCCEECCCC*****C
***CCHHHCCC*-*CCCCCCCCCC*-**HHHCCEECCCCCCCCCEECCCC-----C

57492.tem
_________________________________
---CCHHHCCCH-HCCCCCCCCCCH-HHHHHCCEECCCCCCCCCEECCCC-----C




Structural block scores
0	2	-	3.0	P	  75.0  8.7

3	4	C	5.0	H	  6.0  8.8

5	7	H	5.0	H	  3.7  5.8

8	10	C	5.0	H	  6.5  5.0

14	23	C	5.0	H	  4.0  4.9

26	30	H	3.8	M	  5.0  5.5

31	32	C	5.0	H	  6.2  4.0

33	34	E	5.0	H	  0.5  1.0

35	43	C	5.0	H	  5.1  5.2

44	45	E	5.0	H	  0.0  0.0

46	49	C	5.0	H	  4.5  6.6

50	54	-	3.0	P	  7.2  75.0

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