Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2jo1a-
CCC---CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHCCCCCCCCCCCHHHHHCHHHHCCC-----

>P1;d2jp3a-
CCCCCCC------CHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCC------CCCCCCCHHHHCCCCCCC
PSA

>P1;d2jo1a-
b66---96a88697869a996598677659766456587676566659aa39b39939a824874568577956a-----

>P1;d2jp3a-
e79967b------67837556-7889759877978886775a68754764787359------865276355966775a8d


Translating the sequences
CCC---C******C**HHHHH*HHHHHHHHHHHHHHHHHHHHHHHHH*HHH*CCCC******HHHHHCHHHH*CC-----
CCC***C------CHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH**HHHHHHCCCC------*****C*HHHHCC*****

310576.tem
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CCC---C------CHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC------HHHHHCHHHHHCC-----




Structural block scores
0	2	C	5.0	H	  7.8  10.2

3	5	-	3.0	P	  75.0  7.3

7	12	-	3.0	P	  7.9  75.0

14	20	H	4.4	M	  8.2  5.9

22	51	H	4.7	H	  6.7  7.1

52	55	C	5.0	H	  8.1  6.0

56	61	-	3.0	P	  6.1  75.0

62	66	H	3.0	P	  6.0  5.6

68	72	H	4.2	M	  6.6  5.6

73	74	C	5.0	H	  8.2  6.5

75	79	-	3.0	P	  75.0  8.8

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