Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2b9da1
---CEEEEEEECCCCCCEEEEEEECCHHHHHHHHHHHC-CCCCCCCCCCCCCC

>P1;d2ewla1
CCCCEEEEEEECCCCCCEEEEEEECCHHHHHHHHHHHHHCCCCCCHHHHHHC-
PSA

>P1;d2b9da1
---77470323026176516472737884188347408-94623074067986

>P1;d2ewla1
b56564505150743866121543166a52772555084a643517705858-


Translating the sequences
---CEEEEEEECCCCCCEEEEEEECCHHHHHHHHHHH*-CCCCCC******C*
***CEEEEEEECCCCCCEEEEEEECCHHHHHHHHHHHH*CCCCCCHHHHHHC-

161234.tem
_________________________________
---CEEEEEEECCCCCCEEEEEEECCHHHHHHHHHHHH-CCCCCCHHHHHHC-




Structural block scores
0	2	-	3.0	P	  75.0  7.5

4	10	E	5.0	H	  3.7  3.7

11	16	C	5.0	H	  3.7  4.7

17	23	E	5.0	H	  4.6  3.1

24	25	C	5.0	H	  5.0  3.5

26	37	H	4.8	H	  5.2  5.2

39	44	C	5.0	H	  4.0  4.9

45	50	H	3.0	P	  5.5  5.3

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