Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1j5ya2
-CCCEEEEEEEECCHHHHHHHHHHHHHCCCEEEEEEEEECCCEEEEEEEEECCHHHHHHHHHC-CCCCCCCC-CHHHHEEEEEEEECCCCC--CCCCHHHHCCCCCCC-

>P1;d7cv2a2
CCCCEEEEEEEECCCCCHHHHHHHHHCCCCEEEEEEEEECCCEEEEEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHHHCCCCCCCC
PSA

>P1;d1j5ya2
-45835851406061953550010006250202012082767b62567060154740563199-88a97540-514b15030202136790--740620673902269-

>P1;d7cv2a2
c7a4153603030699435500310043a01041010825878634471507678404430562876a16412a4181304010207568306601820774a013ab9


Translating the sequences
-CCCEEEEEEEECCHHHHHHHHHHHHHCCCEEEEEEEEECCCEEEEEEEEECCHHHHHHHHH*-**CCCCCC-CHHHHEEEEEEEECC***--****HHHHCCCCCCC-
*CCCEEEEEEEECC***HHHHHHHHH*CCCEEEEEEEEECCCEEEEEEEEECCHHHHHHHHHH*HHCCCCCC*C****EEEEEEEECCHHH**HHHHHHHHCCCCCCC*

75500.tem
_________________________________
-CCCEEEEEEEECCHHHHHHHHHHHHHCCCEEEEEEEEECCCEEEEEEEEECCHHHHHHHHHH-HHCCCCCC-CHHHHEEEEEEEECCHHH--HHHHHHHHCCCCCCC-




Structural block scores
1	3	C	5.0	H	  5.7  7.2

4	11	E	5.0	H	  4.0  2.6

12	13	C	5.0	H	  3.0  3.0

14	26	H	4.4	M	  2.7  3.3

27	29	C	5.0	H	  2.3  4.5

30	38	E	5.0	H	  1.9  1.9

39	41	C	5.0	H	  6.7  6.7

42	50	E	5.0	H	  4.8  4.2

51	52	C	5.0	H	  3.0  6.5

53	62	H	4.8	H	  4.8  4.1

64	65	H	3.0	P	  8.0  7.5

66	71	C	5.0	H	  5.9  4.8

74	77	H	3.0	P	  4.4  3.5

78	85	E	5.0	H	  1.6  1.2

86	87	C	5.0	H	  4.5  6.0

88	90	H	3.0	P	  5.3  5.7

91	92	-	3.0	P	  75.0  3.0

93	100	H	4.0	M	  4.0  3.9

101	107	C	5.0	H	  4.4  5.8

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