Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1bhpa-
CEEECCHHHHHHHHHHCC-CCCHHHHHHHCCEEECCCCCCCCCCCC

>P1;d3nira-
CEECCCHHHHHHHHHHHCCCCCHHHHHHHHCCEECCCCCCCCCCCC
PSA

>P1;d1bhpa-
510056892294079347-9286970097080612b9a91496145

>P1;d3nira-
51002689025608813868363780098090342998a24b9255


Translating the sequences
CEEECCHHHHHHHHHH*C-CCCHHHHHHH*CEEECCCCCCCCCCCC
CEE*CCHHHHHHHHHHHC*CCCHHHHHHHHC*EECCCCCCCCCCCC

57429.tem
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CEEECCHHHHHHHHHHHC-CCCHHHHHHHHCEEECCCCCCCCCCCC




Structural block scores
1	3	E	4.3	M	  0.3  0.3

4	5	C	5.0	H	  5.5  4.0

6	16	H	4.8	H	  5.2  4.5

19	21	C	5.0	H	  6.3  5.7

22	29	H	4.8	H	  4.8  4.4

31	33	E	4.3	M	  2.3  2.3

34	45	C	5.0	H	  6.0  6.4

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