Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1v1ha1
CCCCHHHCEEEECCEEEECCCCCEEECCCCCCCCCCCCEEECCCCCEEECCCCCEEECCCCCCEECCCCCEECC--

>P1;d2oj5b1
-------------------------------------------------------CCCCCCCEEEEC-CEEEECCC
PSA

>P1;d1v1ha1
7a0758684538ba744460aa743436a3b608972533361ab84433987744461abb3645c7864383--

>P1;d2oj5b1
-------------------------------------------------------39808655354a-99658189


Translating the sequences
*******************************************************EECCCCC*EE*C*C*EE*C--
-------------------------------------------------------**CCCCCEEEEC-CEEEEC**

51225.tem
_________________________________
-------------------------------------------------------EECCCCCEEEEC-CEEEEC--




Structural block scores
0	54	-	3.0	P	  5.9  75.0

55	56	E	3.0	P	  4.0  6.0

57	61	C	5.0	H	  8.1  5.4

62	65	E	4.0	M	  4.5  4.2

69	72	E	4.0	M	  5.2  7.0

74	75	-	3.0	P	  75.0  8.5

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