Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1jhna3
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCC

>P1;d1k91a1
---------------------------------CCCEEECCCCCCCCCCCCC-------------------------------CC--CCCCCCEEECCCCCC---------------------
PSA

>P1;d1jhna3
c8a3697788394a22368252684943b928b1655333792935b9146a25653658456ba25975992916570771b04302a1935458069434272554b784466375a37bb

>P1;d1k91a1
---------------------------------4576352791954a9266b-------------------------------87--892945659056689---------------------


Translating the sequences
*********************************CCCEEECCCCCCCCCCCCC*******************************CC**CCCCCCEEECCCCCC*********************
---------------------------------CCCEEECCCCCCCCCCCCC-------------------------------CC--CCCCCCEEECCCCCC---------------------

63887.tem
_________________________________
---------------------------------CCCEEECCCCCCCCCCCCC-------------------------------CC--CCCCCCEEECCCCCC---------------------




Structural block scores
0	32	-	3.0	P	  6.4  75.0

33	35	C	5.0	H	  4.0  5.3

36	38	E	5.0	H	  3.7  4.7

39	51	C	5.0	H	  6.2  6.3

52	82	-	3.0	P	  5.8  75.0

83	84	C	5.0	H	  2.0  7.5

85	86	-	3.0	P	  1.5  75.0

87	92	C	5.0	H	  5.1  6.2

93	95	E	5.0	H	  5.7  6.7

96	101	C	5.0	H	  4.3  5.7

102	122	-	3.0	P	  6.2  75.0

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