Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2jrxa1
CCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCC

>P1;d2otaa1
------CC--CCC-CHHHHHHHHHHCCCCHHHHC-CHHHHHHHHHC-CCCHHHHHHHHHHHHHHCC---------
PSA

>P1;d2jrxa1
87ab286569856a767745851766805995187649a437761465356a74a855875487687889a9a9b

>P1;d2otaa1
------89--759-5578656819979088a617-549a6388616-6369964974468569969---------


Translating the sequences
******CC**HHH*HHHHHHHHHHHHCCCHHHHH*HHHHHHHHHHH*HCC***HHHHHHHHHHHHH*********
------CC--***-*HHHHHHHHHH*CCCHHHH*-*HHHHHHHHH*-*CCHHHHHHHHHHHHHH**---------

158651.tem
_________________________________
------CC--HHH-HHHHHHHHHHHHCCCHHHHH-HHHHHHHHHHH-HCCHHHHHHHHHHHHHHHH---------




Structural block scores
0	5	-	3.0	P	  7.8  75.0

6	7	C	5.0	H	  5.5  8.5

8	9	-	3.0	P	  7.5  75.0

10	12	H	3.0	P	  6.3  7.0

14	25	H	4.7	H	  5.8  6.3

26	28	C	5.0	H	  4.3  5.7

29	33	H	4.6	H	  6.4  6.5

35	45	H	4.6	H	  5.6  6.0

48	49	C	5.0	H	  4.0  4.5

50	65	H	4.4	M	  6.8  6.9

66	74	-	3.0	P	  9.2  75.0

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