Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d3bypa1
CCCHHHHHHHHHHHCCCCCCCCEEEEEEEEEECCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECC--

>P1;d3h90a2
CCCHHHHHHHHHHHHHCC-CCCEEEEEEEEEECCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCC
PSA

>P1;d3bypa1
505971175048208609c404604607066688612040301066716a760660043037205920850605043366c--

>P1;d3h90a2
306981462046105838-6075033160637a852204030107682589616710440362037507a060706214683b


Translating the sequences
CCCHHHHHHHHHHH**CC*CCCEEEEEEEEEECCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECC--
CCCHHHHHHHHHHHHHCC-CCCEEEEEEEEEECCEEEEEEEEE*CCCCCHHHHHHHHHHHHHHHHHHCCC*EEEEEEE*CC**

160240.tem
_________________________________
CCCHHHHHHHHHHHHHCC-CCCEEEEEEEEEECCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECC--




Structural block scores
0	2	C	5.0	H	  3.3  3.0

3	15	H	4.7	H	  4.5  4.2

16	17	C	5.0	H	  4.5  5.5

19	21	C	5.0	H	  2.7  4.3

22	31	E	5.0	H	  4.1  3.4

32	33	C	5.0	H	  8.0  9.2

34	43	E	4.8	H	  1.7  1.7

44	48	C	5.0	H	  5.2  5.6

49	66	H	5.0	H	  3.9  4.0

67	69	C	5.0	H	  4.3  5.8

70	78	E	4.6	H	  3.0  2.9

79	80	C	5.0	H	  9.2  7.0

81	82	-	3.0	P	  75.0  7.2

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