Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2p6va1
CCHHHHHHHHCCCHHHHHCCCCCCCCHHHHHHC-CHHHHHHCC-CCHHHHHHHHHHHCCCCCCCCHHHHC-CCHHHHHHCCC---------CHHHHHHHCC---------

>P1;d2pp4a1
---CHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCC
PSA

>P1;d2p6va1
a79956577310a2036107047957a812840-610250063-27185006501822b59668a03430-60064129618---------7076218914---------

>P1;d2pp4a1
---4870266058008604820885848106503810310043827384018402920b681877045114614651388138406a494b13621085018439967ca


Translating the sequences
***HHHHHHH***HHHHH*******CHHHHHH*-*HHHHHHCC-CCHHHHHHHHHHH*CCCCCCCHHHH*-**HHHHHH***---------*HHHHHHH**---------
---*HHHHHHHHHHHHHHHHHHHHHC**HHHHH*HHHHHHHCC*CCHHHHHHHHHHHHCCCCCCCHHHHH*HHHHHHHHHHH*********HHHHHHHHHH*********

158553.tem
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---HHHHHHHHHHHHHHHHHHHHHHCHHHHHHH-HHHHHHHCC-CCHHHHHHHHHHHHCCCCCCCHHHHH-HHHHHHHHHHH---------HHHHHHHHHH---------




Structural block scores
0	2	-	3.0	P	  8.8  75.0

3	24	H	4.0	M	  4.4  4.3

26	32	H	4.1	M	  4.8  3.4

34	40	H	4.7	H	  2.0  1.9

41	42	C	5.0	H	  4.5  3.5

44	45	C	5.0	H	  4.5  4.5

46	57	H	4.8	H	  3.2  3.4

58	64	C	5.0	H	  8.0  6.9

65	69	H	4.6	H	  2.0  2.2

71	81	H	4.1	M	  3.9  4.2

82	90	-	3.0	P	  75.0  6.3

91	100	H	4.4	M	  4.5  2.7

101	109	-	3.0	P	  75.0  7.7

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