Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2fmaa1
CEEEEEECCCCCCCHHHHHHHHHHHHHHC------CEEEEEEEEEEEECCCEEEEEEEEEEEC

>P1;d2m05a1
CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCCCCCEEEEEEECC
PSA

>P1;d2fmaa1
47625434975234593034205710685------8270772812572aa7424004030267

>P1;d2m05a1
364552559b3232596058304830676429ba670526516235828b732200303003c


Translating the sequences
CEEEEEECCCCCCCHHHHHHHHHHHHHHC------CEEEEEEEEEEEECCCEEEEEEEEEEEC
CEEEEEECCCCCCCHHHHHHHHHHHHHHC******C*EEEEEEE****CCC***EEEEEEE*C

89811.tem
_________________________________
CEEEEEECCCCCCCHHHHHHHHHHHHHHC------CEEEEEEEEEEEECCCEEEEEEEEEEEC




Structural block scores
1	6	E	5.0	H	  4.5  4.5

7	13	C	5.0	H	  4.9  5.1

14	27	H	5.0	H	  3.8  4.6

29	34	-	3.0	P	  75.0  7.2

36	47	E	4.2	M	  4.2  3.8

48	50	C	5.0	H	  9.3  8.8

51	61	E	4.3	M	  2.3  1.5

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