Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1d5ka-
-CCEEEEEEEEEECCCCCCHHHHHHHHHHHCCCCCEECCCCEEECCCCCEEEEEEEEECCCCHHHHHHHHHHCCCCCCEEEEEEEEEEEC

>P1;d2b7cb-
CCCEEEEEEEEECCCCCCCHHHHHHHHHCCCCCCEEEEEEEEEEEECCEEEEEEEEEEECCCCCHHHHHHHHCCCCCCCCEEEEEEEEEC
PSA

>P1;d1d5ka-
-8664030030207559073840384047000712744623755548702000020323b28b4372197429a12b5090719346538

>P1;d2b7cb-
b584220101020455816285007504739281080693713637ab341020503024a405196028304837a1045063364897


Translating the sequences
-CCEEEEEEEEEECCCCCCHHHHHHHHHHHCCCC*EE****EEE**CC*EEEEEEEEE*CCCHHHHHHHHHHCCCCCCEEEEEEEEEEEC
*CCEEEEEEEEE*CCCCCCHHHHHHHHH**CCCCEEEEEEEEEEEECCEEEEEEEEEEECCC**HHHHHHHHCCCCCC**EEEEEEEEEC

54984.tem
_________________________________
-CCEEEEEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEEEEEEEECCEEEEEEEEEEECCCHHHHHHHHHHCCCCCCEEEEEEEEEEEC




Structural block scores
1	2	C	5.0	H	  7.0  6.5

3	12	E	4.8	H	  1.8  1.2

13	18	C	5.0	H	  5.5  4.8

19	29	H	4.6	H	  3.7  3.7

30	33	C	5.0	H	  2.0  5.0

34	45	E	3.8	M	  4.5  4.4

46	47	C	5.0	H	  7.5  11.0

48	58	E	4.6	H	  1.1  1.8

59	61	C	5.0	H	  7.2  6.2

62	71	H	4.6	H	  5.0  3.4

72	77	C	5.0	H	  6.5  5.6

78	88	E	4.6	H	  4.3  4.4

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