Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2hbaa1
CEEEECCCCCCCCCCCCEEECCHHHHHHCCCCCCCEEECCH-HHHHHHHHHHC

>P1;d3bsua1
CEEEEEE-----CCCCEEECCHHHHHHHHCCCCCCEEEEECCHHHHHHHHHC-
PSA

>P1;d2hbaa1
240104662ab217675348186930695027481054049-83287277678

>P1;d3bsua1
7200035-----0476201764a50571038288063551965a60481078-


Translating the sequences
CEEEE*******CCCC*EEEC*HHHHHH*CCCCCCEEE**H-HHHHHHHHHH*
CEEEEEE-----CCCCEEE*CHHHHHHHHCCCCCCEEEEE**HHHHHHHHH*-

55658.tem
_________________________________
CEEEEEE-----CCCCEEEECHHHHHHHHCCCCCCEEEEEH-HHHHHHHHHH-




Structural block scores
1	6	E	4.3	M	  2.5  1.7

7	11	-	3.0	P	  6.4  75.0

12	15	C	5.0	H	  5.2  4.2

16	19	E	4.0	M	  5.0  2.5

21	28	H	4.5	M	  5.8  4.1

29	34	C	5.0	H	  3.7  4.8

35	39	E	4.2	M	  2.6  4.0

42	51	H	4.8	H	  5.7  5.0

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