Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1hlra6
CC-CCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCC

>P1;d1n62a1
CCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCC--CCCCCCCCCHHHHHHHHHHHHHHHCCCCCC------------------------------

>P1;d3eubs2
CCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHCCC--CCCCCCCCCHHHHHHHHCC-----------------------------------------

>P1;d5y6qa2
CCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHCC--CCCCCCCCHHHHHHHHHHHHHHHCC-----------------------------------
PSA

>P1;d1hlra6
83-a914101200122800460a204a0092058006647607484067208838180a30a4820030033002042a56647405174397664992941485043100555

>P1;d1n62a1
498a656104300752603463a2179017305600653550459504a208--b290920a383004001200365297754b------------------------------

>P1;d3eubs2
7898934604440672903563a31790162036116847807695067219--b190a30a57003720752-----------------------------------------

>P1;d5y6qa2
8b97854305400562603564a31690184036019593197493057507--c290a37056500500550274367-----------------------------------


Translating the sequences
CC-CCCCHHHHHHHH*CCCCCCCCHHHHHHHHHHHH**CCCCCHHHHHHH****CCCCCCCCCHHHHHHHHHHHHHH*C***********************************
CCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHH*CCCCCHHHHHHHCC--CCCCCCCCCHHHHHHHHHHHHHH*C*****------------------------------
CCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHH*CCCCCHHHHHH*CC--CCCCCCCCCHHHHHHHH**-----------------------------------------
CCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHH*CCCCCHHHHHHHCC--CCCCCCCC*HHHHHHHHHHHHHH*C-----------------------------------

47741.tem
_________________________________
CCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHH*CCCCCHHHHHHHCC--CCCCCCCCCHHHHHHHHHHHHHH*C*****------------------------------




Structural block scores
0	6	C	4.9	H	  15.8  6.9  6.9  7.5

7	14	H	5.0	H	  0.9  2.5  3.9  2.9

15	23	C	4.9	H	  3.6  4.1  4.6  4.4

24	36	H	4.9	H	  3.4  3.5  3.3  3.7

38	42	C	5.0	H	  4.8  3.4  5.2  5.8

43	49	H	4.9	H	  4.4  5.1  5.0  4.7

50	51	C	4.3	M	  4.0  4.0  5.0  3.5

52	53	-	4.3	M	  5.5  75.0  75.0  75.0

54	62	C	4.9	H	  5.0  5.2  5.6  5.4

63	76	H	4.7	H	  1.8  2.3  23.8  3.0

79	83	*	3.5	M	  5.6  6.9  75.0  75.0

84	113	-	4.3	M	  4.3  75.0  75.0  75.0

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