Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2ywwa2
CEEECCCCCCCCCCHHHCCCCCCEEEEEEC-CCCEEEECCCCCCCC--CCCC-

>P1;d4fywb2
CEEECCCCCCCCCCCCCCCCCCCEEEEEECCCCEEEEECCCCCEEEHHHHHCC
PSA

>P1;d2ywwa2
8526450501289040257a3714040246-a75503043177308--7437-

>P1;d4fywb2
a4447816023ab070384836100426849b24004052176222276067b


Translating the sequences
CEEECCCCCCCCCCHHHCCCCCCEEEEEEC-CC*EEEECCCCC***--***C-
CEEECCCCCCCCCC***CCCCCCEEEEEEC*CCEEEEECCCCCEEE**HHHC*

57825.tem
_________________________________
CEEECCCCCCCCCCHHHCCCCCCEEEEEEC-CCEEEEECCCCCEEE--HHHC-




Structural block scores
1	3	E	5.0	H	  4.3  4.0

4	13	C	5.0	H	  3.4  4.9

14	16	H	3.0	P	  2.0  3.3

17	22	C	5.0	H	  5.6  5.0

23	28	E	5.0	H	  2.3  3.3

31	32	C	5.0	H	  8.8  6.8

33	37	E	4.6	H	  2.6  1.6

38	42	C	5.0	H	  4.4  4.2

43	45	E	3.0	P	  3.7  2.0

46	47	-	3.0	P	  75.0  4.5

48	50	H	3.0	P	  4.7  4.0

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