Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1o75a1
CCCCCEEEEEEECCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHCCEEEEEEEECCCCCCCCCCCEEECCCCCCCEECCCCCCCEEEEEECCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEEC

>P1;d1o75a2
--CCCCCCCEEEEE-------EEEEEEECCC-----------CCCCCCE-EEEEEEC--------CCCCCEEE----EEECCE-EEEEEEEECC---------CCEEEEEEECCCCCCEEEEEEC-
PSA

>P1;d1o75a1
84a5003247174a7564b8140000020332655a0648302600640540501103936717846420a06385000287a8623000002294b309b0251203010408b04504040508

>P1;d1o75a2
--8919a9180709-------a430405608-----------7810570-200021a--------c7953049----390737-7180b27077---------9450002030573a33666150-


Translating the sequences
**CCCEEEEEEE**********EEEEEEEEE***********HHHHCCE*EEEEEEC********CCEEE*******EE*CC****EEEEEECC*********CEEEEEEEEECCCCCEEEEEEE*
--CCC****EEEEE-------EEEEEEE***-----------****CCE-EEEEEEC--------CC***EEE----EEECCE-EEEEEEEECC---------C*EEEEEEE*CCCCCEEEEEE*-

81986.tem
_________________________________
--CCCEEEEEEEEE-------EEEEEEEEEE-----------HHHHCCE-EEEEEEC--------CCEEEEEE----EEECCE-EEEEEEEECC---------CEEEEEEEEECCCCCEEEEEEE-




Structural block scores
0	1	-	3.0	P	  6.0  75.0

2	4	C	5.0	H	  5.2  6.0

5	13	E	3.7	M	  4.3  5.9

14	20	-	3.0	P	  6.1  75.0

21	30	E	4.2	M	  1.2  4.0

31	41	-	3.0	P	  4.5  75.0

42	45	H	3.0	P	  2.0  4.0

46	47	C	5.0	H	  5.0  6.0

50	55	E	5.0	H	  1.8  0.8

57	64	-	3.0	P	  5.5  75.0

65	66	C	5.0	H	  5.0  9.8

67	72	E	3.0	P	  3.8  5.0

73	76	-	3.0	P	  4.0  75.0

77	79	E	4.3	M	  0.7  4.0

80	81	C	5.0	H	  7.5  5.0

84	91	E	4.5	M	  1.4  4.6

92	93	C	5.0	H	  2.0  7.0

94	102	-	3.0	P	  5.6  75.0

104	112	E	4.6	H	  1.2  1.6

113	117	C	5.0	H	  5.7  5.7

118	124	E	4.7	H	  1.9  3.9

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