Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2ckaa1
----------CCCCCCCCCCEEECCCCCEECHHHCCCHHHHHHHHHHCCCEEECHHHHHHHHHHCCCC-------------------

>P1;d2v0fa1
CCCCHHHCCHHHCCCCCCCCEEECCCCCEECCCCCCCHHHHHHHHHHCCCEEECHHHHHHHHHCCCCCHHHHHHCCCCCCCCCCCCC
PSA

>P1;d2ckaa1
----------c4075744010315a845237b9701733507832aa5361220580473267692a5-------------------

>P1;d2v0fa1
6822097476b51a08050000148606020878003063027108736510001401600480a2058912a203aa0847a8aad


Translating the sequences
----------**CCCCCCCCEEECCCCCEECHHHCCCHHHHHHHHHHCCCEEECHHHHHHHHHHCCCC-------------------
**********HHCCCCCCCCEEECCCCCEEC***CCCHHHHHHHHHHCCCEEECHHHHHHHHH*CCCC*******************

160481.tem
_________________________________
----------HHCCCCCCCCEEECCCCCEECHHHCCCHHHHHHHHHHCCCEEECHHHHHHHHHHCCCC-------------------




Structural block scores
0	9	-	3.0	P	  75.0  5.1

10	11	H	3.0	P	  8.2  8.2

12	19	C	5.0	H	  3.5  3.1

20	22	E	5.0	H	  1.3  0.3

23	27	C	5.0	H	  6.5  4.8

28	29	E	5.0	H	  2.5  1.0

31	33	H	3.0	P	  9.2  7.7

34	36	C	5.0	H	  2.7  1.0

37	46	H	5.0	H	  5.2  3.4

47	49	C	5.0	H	  4.7  4.7

50	52	E	5.0	H	  1.7  0.3

54	63	H	4.8	H	  4.8  2.4

64	67	C	5.0	H	  6.6  4.4

68	86	-	3.0	P	  75.0  6.8

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