Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1eija-
--------------------CCCCCCCCCHHHHH---HHCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHC--CCC--------

>P1;d2crua1
CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCC
PSA

>P1;d1eija-
--------------------b9bbba78654068---3405970483069038537501870374065025467850001286056007612--899--------

>P1;d2crua1
b98a9b99aa68ba498987988767763564862136004b50484075049745a306502730172077781a96165b70361056262b5a83b8988b9


Translating the sequences
--------------------*********HHHHH---HHCCHHHHHHHHHH***CHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHC--CCC--------
********************HHHHHHHHHHHHHH***HHCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHC**CCC********

46950.tem
_________________________________
--------------------HHHHHHHHHHHHHH---HHCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHC--CCC--------




Structural block scores
0	19	-	3.0	P	  75.0  9.0

20	33	H	3.7	M	  7.8  6.4

34	36	-	3.0	P	  75.0  2.0

37	38	H	5.0	H	  3.5  3.0

39	40	C	5.0	H	  2.5  2.0

41	53	H	4.5	M	  4.8  5.0

55	71	H	5.0	H	  3.8  3.9

72	79	C	5.0	H	  3.4  6.1

80	90	H	5.0	H	  3.7  4.2

92	93	-	3.0	P	  75.0  6.8

94	96	C	5.0	H	  8.7  7.8

97	104	-	3.0	P	  75.0  8.5

>>>>>>