Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1pjua2
CCCCCCCCCCEEECCCCCCCEECCCCCCCCCCCCCCCEEECCCCCEEEECCCCCCC-------------------

>P1;d4sgbi-
------------------------CCCCCCCCCCCCCEEECCCCCEEEECCCCCCCCCCCCCCCCCCCCEEECCC
PSA

>P1;d1pjua2
b19a85391130506a168961670c622334034205022676854140639077-------------------

>P1;d4sgbi-
------------------------845212230657130127a475214051259854b0788527702426369


Translating the sequences
************************CCCCCCCCCCCCCEEECCCCCEEEECCCCCCC-------------------
------------------------CCCCCCCCCCCCCEEECCCCCEEEECCCCCCC*******************

100897.tem
_________________________________
------------------------CCCCCCCCCCCCCEEECCCCCEEEECCCCCCC-------------------




Structural block scores
0	23	-	3.0	P	  5.3  75.0

24	36	C	5.0	H	  3.2  3.5

37	39	E	5.0	H	  2.3  1.3

40	44	C	5.0	H	  5.8  6.1

45	48	E	5.0	H	  3.5  3.0

49	55	C	5.0	H	  4.6  4.3

56	74	-	3.0	P	  75.0  5.1

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