Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2foma1
CCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCC----

>P1;d6y3ba-
-CCCCCCCCCCCCCCCC-----CCCCCCCCEEECCCCCEEEC
PSA

>P1;d2foma1
9895a47845b5826378599094747b64a866a875----

>P1;d6y3ba-
-9a6b87977b89866b-----b9ba47594656b8776877


Translating the sequences
*CCCCCCCCCCCCCCHH*****CCCCCCCC***CCCCC----
-CCCCCCCCCCCCCC**-----CCCCCCCCEEECCCCC****

310588.tem
_________________________________
-CCCCCCCCCCCCCCHH-----CCCCCCCCEEECCCCC----




Structural block scores
1	14	C	5.0	H	  6.6  8.4

15	16	H	3.0	P	  5.0  8.8

17	21	-	3.0	P	  6.2  75.0

22	29	C	5.0	H	  6.6  8.4

30	32	E	3.0	P	  8.2  5.0

33	37	C	5.0	H	  7.3  7.9

38	41	-	3.0	P	  75.0  7.0

>>>>>>