Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1ev0a-
CHHHCCCCHHHHHHHHHHHHHHHCCCCHHHEEEEEEECCCCCEEEEEEECCCCCCCCC

>P1;d6u6sa-
------CCHHHHHHHHHHHHHHHCCCCHHHEEEEEEEECC-EEEEEEEECC-------
PSA

>P1;d1ev0a-
9615929631662434275147767076a307143574b9a76515372854978b9a

>P1;d6u6sa-
------b84485372324413774b066a6070627779a-8473526295-------


Translating the sequences
******CCHHHHHHHHHHHHHHHCCCCHHHEEEEEEE*CC**EEEEEEECC*******
------CCHHHHHHHHHHHHHHHCCCCHHHEEEEEEEECC-EEEEEEEECC-------

55229.tem
_________________________________
------CCHHHHHHHHHHHHHHHCCCCHHHEEEEEEEECC-EEEEEEEECC-------




Structural block scores
0	5	-	3.0	P	  5.3  75.0

6	7	C	5.0	H	  7.5  9.8

8	22	H	5.0	H	  4.1  4.3

23	26	C	5.0	H	  5.0  5.4

27	29	H	5.0	H	  6.5  7.5

30	37	E	4.8	H	  3.9  4.5

38	39	C	5.0	H	  10.2  9.8

41	48	E	4.8	H	  4.5  4.6

49	50	C	5.0	H	  6.5  7.0

51	57	-	3.0	P	  8.4  75.0

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