Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1ozbi-
-CCCCCCCCCC----------CCCHHHCCCC------C

>P1;d2i9wa2
C-HHHCCCHHHCCCCCCCCCCCCCHHHCCHHHHHHHHC

>P1;d2i9wa3
CCCCCCCCCCCCC---------CCHHHCCCCC------
PSA

>P1;d1ozbi-
-494857064c----------e742362718------b

>P1;d2i9wa2
9-93673065376896b4ba946324613258668a98

>P1;d2i9wa3
c376875054948---------66058240a8------


Translating the sequences
-CCCCCCCCCC----------CCCHHHCCCC------C
C-***CCC***CC********CCCHHHCC********C
CCCCCCCCCCCCC---------CCHHHCCCC*------

103642.tem
_________________________________
CCCCCCCCCCCCC--------CCCHHHCCCC*-----C




Structural block scores
0	12	C	4.2	M	  21.9  10.7  6.0

13	20	-	4.0	M	  75.0  8.7  75.0

21	23	C	4.7	H	  8.5  4.3  29.0

24	26	H	5.0	H	  3.7  4.0  4.3

27	30	C	4.5	M	  4.5  2.8  4.1

32	36	-	4.0	M	  75.0  7.9  75.0

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