Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d4htga2
CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCEEEEEEEEECCCCCCEEEEEEEEECCHHHHHHHHHHHHHHHHC---------------

>P1;d4mlva2
CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCEEEEEEEEC----CHHHHHHHHHHHHHHHCHHHHHHHHHHCCC
PSA

>P1;d4htga2
7755651152027004810a04b93417180432b843040603322888784641535350658502710560065059---------------

>P1;d4mlva2
9686732055027203950604b60206170503cc7301020302256785424351348----60760043008405845026104613784c


Translating the sequences
CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCEEEEEEEEECCCCCCEEEEEEEEE****HHHHHHHHHHHHHH*---------------
CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCC*EEEEEEEECCCCCCEEEEEEEE*----*HHHHHHHHHHHHHH***************

54782.tem
_________________________________
CCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCEEEEEEEEECCCCCCEEEEEEEEE----HHHHHHHHHHHHHHH---------------




Structural block scores
0	1	C	5.0	H	  7.0  7.5

2	17	H	5.0	H	  3.2  4.0

18	25	C	5.0	H	  5.2  3.7

26	32	E	5.0	H	  3.4  2.7

33	36	C	5.0	H	  6.4  8.8

37	45	E	4.8	H	  2.3  1.2

46	51	C	5.0	H	  6.8  5.5

52	60	E	4.8	H	  4.0  3.8

61	64	-	3.0	P	  4.8  75.0

65	79	H	4.7	H	  3.4  3.4

80	94	-	3.0	P	  75.0  4.2

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