Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d4hwxa1
CCCCCCEEEEEEEECCCCCCCEEEEEEEEEECCCEECCCCCHHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCCCCEEEEEEEEECCEEEEEEEEECCHHHHHHHCCCCHHHCC

>P1;d6i0ia-
--CCCCEEEEEEEECCCHHHCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHCCCCHHHHHCC-CCCCCCCCCCCCEEEEEEEEECCEEEEEEEEECCHHHHHHHC--CCCCCC
PSA

>P1;d4hwxa1
c2a3806050201645079a275343060518b7074805525500720680805076015a36995a15767710001053203257161643040742081207a130052

>P1;d6i0ia-
--a370505010075563a70c535316040488173805616500640581907074006b-5bb290987671200104721528917233203045318313--420050


Translating the sequences
**CCCCEEEEEEEECCC***CEEEEEEEEEECCCEECCCCCHHHHHHHHHHCCCCHHHH*CC*CCCCCCCCCCCCEEEEEEEEECCEEEEEEEEECCHHHHHHHC**CHHHCC
--CCCCEEEEEEEECCCHHHCEEEEEEEEE*CCC**CCCCCHHHHHHHHHHCCCCHHHHHCC-CCCCCCCCCCCCEEEEEEEEECCEEEEEEEEECCHHHHHHHC--C***CC

55399.tem
_________________________________
--CCCCEEEEEEEECCCHHHCEEEEEEEEEECCCEECCCCCHHHHHHHHHHCCCCHHHHHCC-CCCCCCCCCCCCEEEEEEEEECCEEEEEEEEECCHHHHHHHC--CHHHCC




Structural block scores
0	1	-	3.0	P	  7.2  75.0

2	5	C	5.0	H	  5.4  5.1

6	13	E	5.0	H	  2.5  2.2

14	16	C	5.0	H	  3.0  5.3

17	19	H	3.0	P	  8.8  6.8

21	30	E	4.8	H	  3.4  4.0

31	33	C	5.0	H	  8.8  6.7

34	35	E	3.0	P	  3.5  4.0

36	40	C	5.0	H	  4.4  4.4

41	50	H	5.0	H	  3.5  3.5

51	54	C	5.0	H	  3.2  4.2

55	59	H	4.6	H	  2.8  2.2

60	61	C	5.0	H	  7.8  8.8

63	74	C	5.0	H	  6.1  6.4

75	83	E	5.0	H	  1.2  1.9

84	85	C	5.0	H	  2.5  3.5

86	94	E	5.0	H	  3.7  3.9

95	96	C	5.0	H	  2.0  1.5

97	103	H	5.0	H	  3.4  3.6

105	106	-	3.0	P	  8.8  75.0

108	110	H	3.0	P	  1.0  0.7

111	112	C	5.0	H	  3.5  2.5

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