Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2izxa-
-------CCC--CHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHC--

>P1;d3im3a-
CHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC
PSA

>P1;d2izxa-
-------869--846755671552177681976972375235657988--

>P1;d3im3a-
9a887867387473a625760775287581a8485226524564787888


Translating the sequences
-------***--CHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH*--
*******HHH**CHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH**

47391.tem
_________________________________
-------HHH--CHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH--




Structural block scores
0	6	-	3.0	P	  75.0  8.1

7	9	H	3.0	P	  7.7  6.0

10	11	-	3.0	P	  75.0  5.5

13	27	H	5.0	H	  4.9  5.4

28	31	C	5.0	H	  6.2  6.9

32	47	H	4.9	H	  5.8  5.2

48	49	-	3.0	P	  75.0  8.0

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