Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1eara2
CEEEEEEECCCHHHHHHHHHHHHHCCCCCEEECCEEEEECCHHHHHHHHHHCCEEEEEEECCCCCCCC

>P1;d1gmua2
CEEEEEEECCCHHHHHHHHHHHHHCCCCCEEECCEEEEECCHHHHHHHHCCCCCEEEEEECCCCCCCC
PSA

>P1;d1eara2
54600004066a73196038309739251034971000644780260067180727545362869399

>P1;d1gmua2
656001081b4882075029108859160142952010544781051047390807446360835bae


Translating the sequences
CEEEEEEECCCHHHHHHHHHHHHHCCCCCEEECCEEEEECCHHHHHHHHHHCCEEEEEEECCCCCCCC
CEEEEEEECCCHHHHHHHHHHHHHCCCCCEEECCEEEEECCHHHHHHHH**CC*EEEEEECCCCCCCC

69737.tem
_________________________________
CEEEEEEECCCHHHHHHHHHHHHHCCCCCEEECCEEEEECCHHHHHHHHHHCCEEEEEEECCCCCCCC




Structural block scores
1	7	E	5.0	H	  2.0  2.9

8	10	C	5.0	H	  4.0  5.5

11	23	H	5.0	H	  5.1  4.5

24	28	C	5.0	H	  4.0  4.2

29	31	E	5.0	H	  2.3  2.3

32	33	C	5.0	H	  8.0  7.0

34	38	E	5.0	H	  1.4  1.6

39	40	C	5.0	H	  4.0  4.0

41	50	H	4.6	H	  3.7  3.6

51	52	C	5.0	H	  4.0  4.5

53	59	E	4.7	H	  4.7  4.6

60	67	C	5.0	H	  6.5  7.3

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