Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2zxea3
CEEEEEEC--CEEEEEEHHHCCCCCEEEEECCCCCCCEEEEEEEE--EEEEECHHHHCCCCCEECCCCCCCC---CCCCCCCEECCCCEEEEEEEEEEEEECHHHCHHHHHHHHC

>P1;d3ar4a2
CEEEEECCCCCCCEEEEHHHCCCCCEEEEECCCCCCCEEEEEEECCCCEEEECHHHHCCCCCEEECCCCCCCCCCCHHHCCCEECCCCEEEECEEEEEEEECHHHCHHHHHHHHC
PSA

>P1;d2zxea3
a612014b--984661429707571301072a4801000404609--b030203405987834404386349---665705020043040355503040453a860311757888

>P1;d3ar4a2
9222033b95a73162638506571301036a37000003044154a5040403600928923307396287891725525010014040342402040442c660151557588


Translating the sequences
CEEEEEEC--CEEEEEEHHHCCCCCEEEEECCCCCCCEEEEEEEE--EEEEECHHHHCCCCCEE*CCCCCCC---C***CCCEECCCCEEEEEEEEEEEEECHHHCHHHHHHHHC
CEEEEE*C**C**EEEEHHHCCCCCEEEEECCCCCCCEEEEEEE****EEEECHHHHCCCCCEEECCCCCCC***CHHHCCCEECCCCEEEE*EEEEEEEECHHHCHHHHHHHHC

81653.tem
_________________________________
CEEEEEEC--CEEEEEEHHHCCCCCEEEEECCCCCCCEEEEEEEE--EEEEECHHHHCCCCCEEECCCCCCC---CHHHCCCEECCCCEEEEEEEEEEEEECHHHCHHHHHHHHC




Structural block scores
1	6	E	4.7	H	  2.3  2.0

8	9	-	3.0	P	  75.0  7.0

11	16	E	4.3	M	  4.8  4.2

17	19	H	5.0	H	  6.0  5.3

20	24	C	5.0	H	  4.0  3.8

25	29	E	5.0	H	  2.2  1.4

30	36	C	5.0	H	  3.6  3.8

37	44	E	4.8	H	  2.9  2.1

45	46	-	3.0	P	  75.0  7.2

47	51	E	4.6	H	  3.3  2.6

53	56	H	5.0	H	  3.0  2.2

57	61	C	5.0	H	  7.0  6.0

62	64	E	4.3	M	  2.7  2.0

65	71	C	5.0	H	  5.3  6.0

72	74	-	3.0	P	  75.0  6.0

76	78	H	3.0	P	  6.0  4.0

79	81	C	5.0	H	  1.7  2.3

82	83	E	5.0	H	  1.0  0.5

84	87	C	5.0	H	  1.8  1.2

88	100	E	4.8	H	  2.9  2.4

102	104	H	5.0	H	  8.2  8.2

106	113	H	5.0	H	  5.0  4.6

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