Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2f4mb2
CCHHHHHCCCHHHHHHHHHHHH-CHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHHHHCCCC

>P1;d2qshx-
-------CCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCCHHHHHHHCHHHHHHHHHCCC
PSA

>P1;d2f4mb2
4540471194780374045028-57a536613761268567137304637a1046006573

>P1;d2qshx-
-------e07b91284016147745853962596058517918834665586167317788


Translating the sequences
*******CCCHHHHHHHHHHHH-CHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHHHH*CCC
-------CCCHHHHHHHHHHHH*CHHHHHHHHHHHHHHC**HHHHHHHCHHHHHHHHHCCC

101238.tem
_________________________________
-------CCCHHHHHHHHHHHH-CHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHHHHHCCC




Structural block scores
0	6	-	3.0	P	  3.6  75.0

7	9	C	5.0	H	  4.7  7.2

10	21	H	5.0	H	  4.0  4.5

24	37	H	5.0	H	  5.1  5.4

39	47	H	4.6	H	  4.1  5.8

49	57	H	4.8	H	  3.8  4.9

58	60	C	5.0	H	  5.0  7.7

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