Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1on2a2
CHHHHHHHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCHHHHH--HHHHHHCC

>P1;d2dtra2
CHHHHHHHHH-CCHHHHHHHHHHHCCCCCHHHHHHHCC-HHHC-CHHHHHHHHHHCCCC--CCCCCCCCCCCHHHCC
PSA

>P1;d1on2a2
a988976685565027002421513-3396a706950594068384940561264075146577337--82588479

>P1;d2dtra2
9998967733-402230101201464835596069207-4278-647705611650917--50147560412860b3


Translating the sequences
CHHHHHHHHH*HHHHHHHHHHHHHC-CCCHHHHHHHHH*HHHH*CHHHHHHHHHHHHHH**CHHHHH--HHHHHHCC
CHHHHHHHHH-**HHHHHHHHHHHC*CCCHHHHHHH**-HHH*-CHHHHHHHHHH****--C**********HHHCC

47979.tem
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CHHHHHHHHH-HHHHHHHHHHHHHC-CCCHHHHHHHHH-HHHH-CHHHHHHHHHHHHHH--CHHHHH--HHHHHHCC




Structural block scores
1	9	H	5.0	H	  7.3  6.8

11	23	H	4.7	H	  2.7  1.5

26	28	C	5.0	H	  5.0  5.3

29	37	H	4.6	H	  5.4  4.9

39	42	H	4.5	M	  4.5  5.2

45	58	H	4.4	M	  3.9  4.2

59	60	-	3.0	P	  5.0  75.0

62	66	H	3.0	P	  5.4  3.4

67	68	-	3.0	P	  75.0  3.0

69	74	H	4.0	M	  5.8  3.5

75	76	C	5.0	H	  8.0  7.2

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