Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1vq8v1
CCCCHHHHHHCCHHHHHHHHHHHHH-HHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC-

>P1;d2j0121
-------------CCCCCHHHHHHH-HHHHHHHHCCCCCCCCCCCCCHHHCCCCCCCCCC---CCCC

>P1;d2qamx1
---CCHHHCCCHHHHHHHHHHHHHCCHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHHCCCCCCCC
PSA

>P1;d1vq8v1
6917495047255860572187156-40873574588a597497b6373075117305701a53a7-

>P1;d2j0121
-------------7a2575187238-50462464467a81b6889624238652549463---a8aa

>P1;d2qamx1
---5a87058465960564057136763661754386b60a-59633572562163067119519ad


Translating the sequences
***C*HHH**C*HHHHHHHHHHHHH-HHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH*****CC-
-------------*****HHHHHHH-HHHHHHHH**CCCCCCC****HHH*********C---CCCC
---C*HHH**C*HHHHHHHHHHHH**HHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHHC***CCCC

46561.tem
_________________________________
---C*HHH**C*HHHHHHHHHHHHH-HHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHC***CCCC




Structural block scores
0	2	-	4.0	M	  5.3  75.0  75.0

5	7	H	4.0	M	  4.7  75.0  5.0

8	9	*	2.7	P	  5.5  75.0  6.5

12	24	H	4.5	M	  4.7  10.8  4.4

26	35	H	4.8	H	  5.1  4.1  4.9

36	42	C	4.9	H	  7.5  7.4  16.3

43	58	H	4.2	M	  4.6  5.2  4.4

60	62	*	2.7	P	  5.5  75.0  5.0

63	66	C	4.5	M	  23.9  9.9  8.5

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