Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1fwoa-
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

>P1;d1i8xa-
CCCCCCCCCCCCCEEEEE-CCC----CCEEEEECC
PSA

>P1;d1fwoa-
b6825a837255c3605713a85b866a042388b

>P1;d1i8xa-
734457847058915125-178----66352356c


Translating the sequences
CCCCCCCCCCCCC******CCC****CC*****CC
CCCCCCCCCCCCCEEEEE-CCC----CCEEEEECC

57277.tem
_________________________________
CCCCCCCCCCCCCEEEEE-CCC----CCEEEEECC




Structural block scores
0	12	C	5.0	H	  6.6  5.5

13	17	E	3.0	P	  4.2  2.8

19	21	C	5.0	H	  7.2  5.3

22	25	-	3.0	P	  7.6  75.0

26	27	C	5.0	H	  8.2  6.0

28	32	E	3.0	P	  3.4  3.6

33	34	C	5.0	H	  9.8  9.2

>>>>>>