Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1rqta-
CCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCC

>P1;d1zavu1
-CCHHHHHHHHHHCCHHHHHHHHHHHHHHCC------
PSA

>P1;d1rqta-
7b8986787447648a95168565743a8778599a9

>P1;d1zavu1
-57896566446838a96577256766777d------


Translating the sequences
*CCHHHHHHHH**CCHHHHHHHHHHHHHHCC******
-CCHHHHHHHHHHCCHHHHHHHHHHHHHHCC------

48300.tem
_________________________________
-CCHHHHHHHHHHCCHHHHHHHHHHHHHHCC------




Structural block scores
1	2	C	5.0	H	  9.8  6.0

3	12	H	4.6	H	  6.6  6.2

13	14	C	5.0	H	  6.0  5.5

15	28	H	5.0	H	  6.3  6.5

29	30	C	5.0	H	  7.0  10.2

31	36	-	3.0	P	  8.4  75.0

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