Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1xoua-
CCCCHHHHHHHHHHHHCCCCCHHHHCCCHHHHHHHHHHHHHC-CHHHHHHHHHHH-CCHHHHHHHHHHCC----------------------------------------

>P1;d1xoub-
--------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCC
PSA

>P1;d1xoua-
4a66497667967774756a5768477a88677765787778-573879456465-86788984747868----------------------------------------

>P1;d1xoub-
--------------------------c8a776878657577767756556767875785776478157617948904652664642568484468755856656778868


Translating the sequences
**************************C*HHHHHHHHHHHHH*-*HHHHHHHHHHH-**HHHHHHHHHH**----------------------------------------
--------------------------CHHHHHHHHHHHHHHH*HHHHHHHHHHHH*HHHHHHHHHHHHHH****************************************

116927.tem
_________________________________
--------------------------CHHHHHHHHHHHHHHH-HHHHHHHHHHHH-HHHHHHHHHHHHHH----------------------------------------




Structural block scores
0	25	-	3.0	P	  6.6  75.0

27	41	H	4.7	H	  7.2  7.0

43	54	H	4.8	H	  5.8  6.3

56	69	H	4.4	M	  7.0  5.6

70	109	-	3.0	P	  75.0  5.8

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