Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1hn6a-
CCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

>P1;d2j4wd1
-------------------------------------------CCEECCHHHHCCCCCCEEEECCCCEEEECCCCCC---------------------------------
PSA

>P1;d1hn6a-
6b5d693411878927571344068367a6b8a99d96730355370002540623247552467b0601306589878698baaa5ab6b677a7788785896a899a

>P1;d2j4wd1
-------------------------------------------7b52775a40904480555279a6441317497a---------------------------------


Translating the sequences
*******************************************CC**CC****CCCCCCEE**CCCC**EECCCCCC*********************************
-------------------------------------------CCEECCHHHHCCCCCCEEEECCCCEEEECCCCCC---------------------------------

82910.tem
_________________________________
-------------------------------------------CCEECCHHHHCCCCCCEEEECCCCEEEECCCCCC---------------------------------




Structural block scores
0	42	-	3.0	P	  6.2  75.0

43	44	C	5.0	H	  4.0  9.2

45	46	E	3.0	P	  3.5  3.5

47	48	C	5.0	H	  0.0  7.0

49	52	H	3.0	P	  2.8  4.9

53	58	C	5.0	H	  4.0  4.2

59	62	E	4.0	M	  4.0  4.2

63	66	C	5.0	H	  6.1  8.1

67	70	E	4.0	M	  2.5  3.0

71	76	C	5.0	H	  6.0  6.4

77	109	-	3.0	P	  8.4  75.0

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