Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2b97a-
----------CCCCCCCCCEEEEEEEEECCCEEEEEECCCCCCCCHHHHHHHHHHCCCEEEEECCCCCEEEEEEEECCCC

>P1;d4aoga1
CCCCCCCCCCCCCC-CCCCEEEEEECCCCCCCCEEEECCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCEECHHHC
PSA

>P1;d2b97a-
----------6104bb7134200046148663025064175907628504810774a061000235764931506407c2

>P1;d4aoga1
b2a98899878308-c82850300341a959236917a053a14a68403500665a1501011865bb58450703891


Translating the sequences
----------CCCC*CCCCEEEEEEEEECCCEEEEEECCCCCCCCHHHHHHHHHHCCCEEEEECCCCCEEEEEEEE***C
**********CCCC-CCCCEEEEEE***CCC**EEEECCCCCCCCHHHHHHHHH*CCCEEEEECCCCC*****EE*HHHC

101751.tem
_________________________________
----------CCCC-CCCCEEEEEEEEECCCEEEEEECCCCCCCCHHHHHHHHHHCCCEEEEECCCCCEEEEEEEEHHHC




Structural block scores
0	9	-	3.0	P	  75.0  8.2

10	13	C	5.0	H	  2.8  4.8

15	18	C	5.0	H	  5.6  7.6

19	27	E	4.3	M	  2.3  2.9

28	30	C	5.0	H	  6.7  7.7

31	36	E	4.3	M	  2.7  4.7

37	44	C	5.0	H	  4.9  5.6

45	54	H	4.8	H	  4.2  3.8

55	57	C	5.0	H	  4.8  5.5

58	62	E	5.0	H	  1.4  1.4

63	67	C	5.0	H	  4.6  6.3

68	75	E	3.5	M	  4.0  5.1

76	78	H	3.0	P	  6.5  6.7

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