Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1pp9h-
CCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCC--------CCCCCCHHHHHHHHHHHHHHHHHHHHHHCC

>P1;d3cx5f-
CCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC
PSA

>P1;d1pp9h-
a7623650476027688045036516806942884a--------a2b37178256503911571077418944c

>P1;d3cx5f-
9963376036713649705623763660474177356598299489347068257603820581076518863c


Translating the sequences
CCCHHHHHHHHH*CCHHHHHHHHHHHHHHHHHH***--------CCCCCCHHHHHHHHHHHHHHHHHHHHHHCC
CCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH********CCCCCCHHHHHHHHHHHHHHHHHHHHHHCC

81531.tem
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CCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH--------CCCCCCHHHHHHHHHHHHHHHHHHHHHHCC




Structural block scores
0	2	C	5.0	H	  7.8  8.0

3	12	H	4.8	H	  3.5  3.9

13	14	C	5.0	H	  6.5  5.0

15	35	H	4.7	H	  5.0  4.7

36	43	-	3.0	P	  75.0  6.5

44	49	C	5.0	H	  5.8  5.2

50	71	H	5.0	H	  4.5  4.6

72	73	C	5.0	H	  8.2  7.8

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