Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2qlvb2
-------CCCCCHHHCCHHHHHHHHHHHCCCCCCCC-------------CCCCCCCCEECCCCCCEEEEEEEEEECCEEEEEEEEEEC

>P1;d2v8qb1
CCCCCCC---------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCEEEEEEEEEECCEEEEEEEEEEC
PSA

>P1;d2qlvb2
-------7a976557557733775676586a9b969-------------676438866568578954221324578a93557477575

>P1;d2v8qb1
d879759---------------78737877889446724873998aacb6a712746347a59a832032235587985757566584


Translating the sequences
-------***************HHHHHHCCCCCCCC-------------CCCCCCCCEECCCCCCEEEEEEEEEECCEEEEEEEEEEC
*******---------------******CCCCCCCC*************CCCCCCCCEECCCCCCEEEEEEEEEECCEEEEEEEEEEC

160219.tem
_________________________________
----------------------HHHHHHCCCCCCCC-------------CCCCCCCCEECCCCCCEEEEEEEEEECCEEEEEEEEEEC




Structural block scores
0	21	-	3.0	P	  28.1  53.8

22	27	H	3.0	P	  6.0  6.7

28	35	C	5.0	H	  8.6  6.6

36	48	-	3.0	P	  75.0  7.8

49	56	C	5.0	H	  6.0  5.4

57	58	E	5.0	H	  5.5  3.5

59	64	C	5.0	H	  7.2  8.3

65	74	E	5.0	H	  3.5  3.3

75	76	C	5.0	H	  9.2  8.0

77	86	E	5.0	H	  5.9  6.2

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