Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1u94a2
CHHHHHHHHHHHCCCEECCCCCEEECCEEEECCHHHHHHHHHHCHHHHHHHHHHHHHHHC

>P1;d1xp8a2
-CHHHHHHHHHHCCCCEEECCEEECCCCEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHC
PSA

>P1;d1u94a2
9521700640272920659b7412069760159497016205845920740373057547

>P1;d1xp8a2
-827900550083700748c66031ab790554487035203747a13670265167479


Translating the sequences
*HHHHHHHHHHHCCCEE**CC*EEECCEEEE*CHHHHHHHHHHCHHHHHHHHHHHHHHHC
-*HHHHHHHHHHCCC*EEECCEEE*CC*EEEECHHHHHHHH**CHHHHHHHHHHHHHHHC

54752.tem
_________________________________
-HHHHHHHHHHHCCCEEEECCEEEECCEEEEECHHHHHHHHHHCHHHHHHHHHHHHHHHC




Structural block scores
1	11	H	4.8	H	  3.1  4.0

12	14	C	5.0	H	  4.3  3.3

15	18	E	3.5	M	  5.0  4.8

19	20	C	5.0	H	  9.2  9.2

21	24	E	4.0	M	  1.8  2.5

25	26	C	5.0	H	  7.5  11.0

27	31	E	4.2	M	  3.8  5.2

33	42	H	4.6	H	  4.2  3.9

44	58	H	5.0	H	  4.1  4.8

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