Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d3s3na1
CHHHHHHHCCCCCCCCCCCCEEEECCEEEEEECCEEEECCCHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHCCCHHHHHHCCCC

>P1;d6vrga1
-----------------------------------------CCCHHHHHHHHHHHHCCCHHHHHHHH----CCC--HHHHHHHHHHCCCCCC-----
PSA

>P1;d3s3na1
9b4076027978297039291465885110526785120037a508710471056733855601760477210180583066128618715787aac

>P1;d6vrga1
-----------------------------------------49a22970582086622937401861----b03--59203700452a82a3-----


Translating the sequences
*****************************************HHHHHHHHHHHHH**CCCHHHHHHHH****CCC**HHHHHHHH**CHHHHH*****
-----------------------------------------***HHHHHHHHHHHHCCCHHHHHHHH----CCC--HHHHHHHHHHC*****-----

46919.tem
_________________________________
-----------------------------------------HHHHHHHHHHHHHHHCCCHHHHHHHH----CCC--HHHHHHHHHHCHHHHH-----




Structural block scores
0	40	-	3.0	P	  4.6  75.0

41	55	H	4.3	M	  4.6  5.2

56	58	C	5.0	H	  4.7  4.3

59	66	H	5.0	H	  3.8  3.8

67	70	-	3.0	P	  5.0  75.0

71	73	C	5.0	H	  0.7  4.8

74	75	-	3.0	P	  4.0  75.0

76	85	H	4.6	H	  4.5  3.5

87	91	H	3.0	P	  5.6  6.8

92	96	-	3.0	P	  9.7  75.0

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