Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1wiba1
CCCCCCCCC-EEEEEEEECCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHCCCCCCCEEEEEEEEEC-CEEEEEECCCCCCCCCCCC

>P1;d3cjsb1
-----CCCEEEEEEEEEECCCCCCCCCHHHHHHCCCCCHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCEEEEEC-----------
PSA

>P1;d1wiba1
a98b48d85-723426750067568a715641940731376007612920793679633030226b-881727238b4ab897a9b

>P1;d3cjsb1
-----a585426181604016064765015203736073460064028405c4aa45030302015665172827-----------


Translating the sequences
*****CCC*-EEEEEEEECCCCCCCCC**HHH*CCCCCHHHHHHHHHHH****CCCEEEEEEEEEC-CEEEEEEC***********
-----CCCE*EEEEEEEECCCCCCCCCHHHHHHCCCCCHHHHHHHHHHHHHHHCCCEEEEEEEEEC*C*EEEEEC-----------

54747.tem
_________________________________
-----CCCE-EEEEEEEECCCCCCCCCHHHHHHCCCCCHHHHHHHHHHHHHHHCCCEEEEEEEEEC-CEEEEEEC-----------




Structural block scores
0	4	-	3.0	P	  8.6  75.0

5	7	C	5.0	H	  9.8  7.8

10	17	E	5.0	H	  4.5  3.5

18	26	C	5.0	H	  5.5  3.9

27	32	H	4.0	M	  4.3  1.8

33	37	C	5.0	H	  3.0  4.6

38	52	H	4.5	M	  4.1  3.9

53	55	C	5.0	H	  7.3  8.3

56	64	E	5.0	H	  2.8  1.6

68	73	E	4.7	H	  4.5  4.2

75	85	-	3.0	P	  9.1  75.0

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