Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2p5ma-
CCCCHHHHHHHHHHHHEEEEEEECCEEEEEECCCCHHHHHHHHHCCCCCCCCEEEECCCEEEEECCCHHHHHHHHHHHHCCC

>P1;d3buea-
----CHHHHHHHHHHHCCEEEEECCEEEEECCCCCHHHHHHHHHHHCCCCEEEEEECCCEEEEEECCCCCHHHHHHHHHCCC
PSA

>P1;d2p5ma-
78775524053408a02460619644050405663077007206709195048070a8340402054483068016504803

>P1;d3buea-
----76a3036003520660838c630305047810960040067091750460809733040305a926067008404944


Translating the sequences
****HHHHHHHHHHHHEEEEEEECCEEEEEECCCCHHHHHHHHH**CCCC**EEEECCCEEEEE*CCHHHHHHHHHHHHCCC
----*HHHHHHHHHHH**EEEEECCEEEEE*CCCCHHHHHHHHHHHCCCCEEEEEECCCEEEEEECC***HHHHHHHHHCCC

55252.tem
_________________________________
----HHHHHHHHHHHHEEEEEEECCEEEEEECCCCHHHHHHHHHHHCCCCEEEEEECCCEEEEEECCHHHHHHHHHHHHCCC




Structural block scores
0	3	-	3.0	P	  7.2  75.0

4	15	H	4.8	H	  3.9  3.8

16	22	E	4.4	M	  4.0  4.4

23	24	C	5.0	H	  5.0  9.2

25	30	E	4.7	H	  2.2  1.8

31	34	C	5.0	H	  5.0  5.0

35	45	H	4.6	H	  3.3  2.9

46	49	C	5.0	H	  6.0  5.5

50	55	E	4.3	M	  3.2  3.0

56	58	C	5.0	H	  7.2  6.3

59	64	E	4.7	H	  1.7  1.7

65	66	C	5.0	H	  4.5  7.8

67	78	H	4.5	M	  3.8  3.8

79	81	C	5.0	H	  3.7  5.7

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