Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1mkca-
---------------CCCEECCCCCCCCCCCCCCCCEECCCCCCCCCCCC--CCCCCCCC---------

>P1;d1mkna-
CCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCEEEECC----------CCCEEECCCCCCCCCCCCC
PSA

>P1;d1mkca-
---------------37690a81a918ba65212152205618328b083--61605317---------

>P1;d1mkna-
968a33357799974bb0806916225951b300452619----------a55341338276664797f


Translating the sequences
---------------CCCEE*CCCCCCCCCCCCC**EECC**********--C***CCCC---------
***************CCCEEECCCCCCCCCCCCCEEEECC----------**CEEECCCC*********

57288.tem
_________________________________
---------------CCCEEECCCCCCCCCCCCCEEEECC------------CEEECCCC---------




Structural block scores
0	14	-	3.0	P	  75.0  6.6

15	17	C	5.0	H	  5.3  7.7

18	20	E	4.3	M	  6.5  4.7

21	33	C	5.0	H	  5.8  4.2

34	37	E	4.0	M	  2.5  4.2

38	39	C	5.0	H	  2.5  5.0

40	51	-	3.0	P	  16.7  63.8

53	55	E	3.0	P	  2.3  2.7

56	59	C	5.0	H	  4.0  4.0

60	68	-	3.0	P	  75.0  8.3

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