Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2rmra-
CCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCC

>P1;d6xawa-
-CHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCC-
PSA

>P1;d2rmra-
b7a69982870256058418a78911830360264387b6186640375038207a48704870783159f

>P1;d6xawa-
-b88876468037405641796792265045036348658374a40464048108c0760172038316b-


Translating the sequences
*C******HHHHHHHHHHCCCCHHHHHHHHHHHHHHH*CCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCC*
-CHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHH**CCC-

47762.tem
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-CHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCC-




Structural block scores
2	17	H	4.2	M	  5.6  5.2

18	21	C	5.0	H	  6.6  5.8

22	37	H	4.9	H	  4.3  4.4

38	41	C	5.0	H	  6.6  5.8

42	52	H	5.0	H	  4.0  4.1

53	56	C	5.0	H	  5.4  5.1

57	66	H	4.6	H	  5.2  3.7

67	69	C	5.0	H	  5.0  6.2

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