Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1udka-
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEECCCC-

>P1;d2z7fi-
CCCCCCCCCCCCCCCCCCC-CCCCCCHHHCCCCCEEEEECC-EEEEECCCCC
PSA

>P1;d1udka-
f638063098956b38bb558590c619605a8400363736541007159-

>P1;d2z7fi-
a6292523b2a473a6aa2-629064045098710005753-02623715a9


Translating the sequences
CCCCCCCCCCCCCCCCCCC*CCCCCC***CCCCCEEE**CC***EEECCCC-
CCCCCCCCCCCCCCCCCCC-CCCCCCHHHCCCCCEEEEECC-EEEEECCCC*

57256.tem
_________________________________
CCCCCCCCCCCCCCCCCCC-CCCCCCHHHCCCCCEEEEECC-EEEEECCCC-




Structural block scores
0	18	C	5.0	H	  7.2  6.2

20	25	C	5.0	H	  6.8  4.5

26	28	H	3.0	P	  5.3  3.0

29	33	C	5.0	H	  5.5  5.0

34	38	E	4.2	M	  2.4  2.4

39	40	C	5.0	H	  5.0  4.0

42	46	E	4.2	M	  2.0  2.6

47	50	C	5.0	H	  5.5  5.9

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