Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2qsba1
CHHHHHHHHHCCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHC-CCC-CCCCCCCHHHHHHHHHHHHHHHHHC-

>P1;d2qzga1
CCCHHHHHHHHHCCHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHCCCC
PSA

>P1;d2qsba1
989566248507305500738603970265066037207598383861076017-069-0737903960475065017206606-

>P1;d2qzga1
c667853186017038027396039602610350271055893a15610740274056138289-2a50673088115606708b


Translating the sequences
CHHHHHHHHH**HHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHH*-***-CCCCC*CHHHHHHHHHHHHHHHHHC-
C**HHHHHHHHH**HHHHCCCCCCHHHHHHHHHHHHH*CCCCCCHHHHHHHHHH*HHH*CCCCC-CHHHHHHHHHHHHHHH**C*

158436.tem
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CHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH-HHH-CCCCC-CHHHHHHHHHHHHHHHHHC-




Structural block scores
1	17	H	4.3	M	  4.3  4.2

18	23	C	5.0	H	  4.5  4.7

24	37	H	4.9	H	  3.8  3.0

38	43	C	5.0	H	  6.7  6.8

44	53	H	4.8	H	  3.9  3.3

55	57	H	3.0	P	  5.0  3.7

59	63	C	5.0	H	  5.2  6.0

66	82	H	4.8	H	  3.8  4.3

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