Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1vq0a2
------CCCCCCCC-CCCCCCC--CCCCCC--CCCEEEECCCCCCEEEECC-CHHHHHHHHHHC

>P1;d1xjha-
CCCCCCCCCCHHHHHHHHHCCCHHHHHHHHCCCCEEEEECCCCCCEEEEEHHHHHHHCC--CCC
PSA

>P1;d1vq0a2
------29264950-7502839--507727--8550323188395515176-408723863a78

>P1;d1xjha-
6984680a36383015203856897066517876408150853213270459107714a--a67


Translating the sequences
------CCCC****-****CCC--******--CC*EEEECCCCCCEEEE**-*HHHHHH**HHC
******CCCCHHHH*HHHHCCC**HHHHHH**CCEEEEECCCCCCEEEEEH*HHHHH**--**C

118352.tem
_________________________________
------CCCCHHHH-HHHHCCC--HHHHHH--CCEEEEECCCCCCEEEEEH-HHHHHHH--HHC




Structural block scores
0	5	-	3.0	P	  75.0  6.8

6	9	C	5.0	H	  4.8  4.9

10	13	H	3.0	P	  4.5  3.5

15	18	H	3.0	P	  3.5  2.5

19	21	C	5.0	H	  6.7  6.3

22	23	-	3.0	P	  75.0  8.5

24	29	H	3.0	P	  4.7  4.2

30	31	-	3.0	P	  75.0  7.5

32	33	C	5.0	H	  6.5  6.5

34	38	E	4.6	H	  2.6  3.6

39	44	C	5.0	H	  5.7  3.2

45	49	E	4.6	H	  3.8  3.2

52	58	H	4.1	M	  4.6  4.4

59	60	-	3.0	P	  4.5  75.0

61	62	H	3.0	P	  8.8  8.2

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