Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1w4ha-
CCCCCCCHHHHHHHHHCCCCHHHCCCCCCCCCCCHHHHHHHHCCC

>P1;d2eq9c-
---CCCCHHHHHHHHHCCCCHHHCCCCCCCCCCCCCCCCCC----
PSA

>P1;d1w4ha-
cbc84238607710764d280870a092bb640468106823869

>P1;d2eq9c-
---36027605630864a15165070649a54045910844----


Translating the sequences
***CCCCHHHHHHHHHCCCCHHHCCCCCCCCCCCHHHHHHH****
---CCCCHHHHHHHHHCCCCHHHCCCCCCCCCCC*******----

47005.tem
_________________________________
---CCCCHHHHHHHHHCCCCHHHCCCCCCCCCCCHHHHHHH----




Structural block scores
0	2	-	3.0	P	  12.2  75.0

3	6	C	5.0	H	  4.2  2.8

7	15	H	5.0	H	  4.7  4.6

16	19	C	5.0	H	  6.9  5.1

20	22	H	5.0	H	  5.0  4.0

23	33	C	5.0	H	  5.3  4.5

34	40	H	3.0	P	  4.4  4.4

41	44	-	3.0	P	  6.5  75.0

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