Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2d9ra1
CCEEEEEECEECCCCCEEEECCCCHHHHHCCCCEEEEEEECCEEEEEEEECCCCCCEEEECHHHHHHHCCCCCCEEEEEEEEC----------------------

>P1;d2nwta1
CCCCCCEEEEC-----CEEEECCCC--CCCC---CCCCCCC-CCCC---------------------------------CCCCCCCCCCCCHHHCCCCCCCCCCC
PSA

>P1;d2d9ra1
a343161405588b9902050427058408856150503039472315034e5760308065401741938194505020443----------------------

>P1;d2nwta1
a967352657c-----5645355a2--b57b---7286955-b499---------------------------------b98cbb7a8b9978a79aa6a999ba


Translating the sequences
CCEEEEEE*EE*****EEEE*CCCH**HHCC***EEEEEEC*EEEE*********************************EEEC----------------------
CC****EEEE*-----*EEEECCC*--**CC---******C-****---------------------------------***C**********************

141694.tem
_________________________________
CCEEEEEEEEE-----EEEEECCCH--HHCC---EEEEEEC-EEEE---------------------------------EEEC----------------------




Structural block scores
0	1	C	5.0	H	  6.8  9.8

2	10	E	3.7	M	  3.2  5.9

11	15	-	3.0	P	  9.1  75.0

16	20	E	4.2	M	  1.4  4.6

21	23	C	5.0	H	  4.3  6.8

25	26	-	3.0	P	  6.5  75.0

27	28	H	3.0	P	  2.0  8.2

29	30	C	5.0	H	  8.0  9.2

31	33	-	3.0	P	  4.0  75.0

34	39	E	3.0	P	  2.2  6.2

42	45	E	3.0	P	  4.0  8.4

46	78	-	3.0	P	  4.0  75.0

79	81	E	3.0	P	  2.7  9.5

83	104	-	3.0	P	  75.0  9.4

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