Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2jqta-
CCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCC--CC

>P1;d4icgc-
---CCCCCCCCCCC----CCCCCC---CCCCCCCCC-CHHHHHHHHCCCCCCCCCCCCC
PSA

>P1;d2jqta-
abb8555750683a758306723781584886a90563055217734674978aa--aa

>P1;d4icgc-
---65962013a38----1a5829---82aa28607-0270050024b56b04a91483


Translating the sequences
***CCHHHHHHHCC****HHHHHH***CCCCCHHHH*HHHHHHHHHHHHHHHCCC--CC
---CC*******CC----******---CCCCC****-*HHHHHHHH******CCC**CC

68989.tem
_________________________________
---CCHHHHHHHCC----HHHHHH---CCCCCHHHH-HHHHHHHHHHHHHHHCCC--CC




Structural block scores
0	2	-	3.0	P	  11.2  75.0

3	4	C	5.0	H	  6.5  5.5

5	11	H	3.0	P	  5.1  4.5

12	13	C	5.0	H	  6.8  5.5

14	17	-	3.0	P	  5.8  75.0

18	23	H	3.0	P	  4.2  5.9

24	26	-	3.0	P	  4.7  75.0

27	31	C	5.0	H	  6.8  6.6

32	35	H	3.0	P	  6.1  5.2

37	51	H	4.1	M	  4.7  3.6

52	54	C	5.0	H	  9.7  7.8

55	56	-	3.0	P	  75.0  2.5

57	58	C	5.0	H	  10.5  5.5

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