Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1vcta2
CC-HHHHHHHHHCCCEEEEEECCCCCCCCCCCHHHHCHHHHHCCEEEEEEECCEEEECCCCCCCCCCCCEEEEEECHHHHHHHHHHHHCCCCCCC

>P1;d2aefa2
CCHHHHHHHHHHCCCEEEEEECC-CCCCCCCCHHHHCHHHHHCCEEEEEECC-CEEECCC-CCCC-CCCEEEEEECC-CC-CCHHHHCC------
PSA

>P1;d1vcta2
67-7647686677b6042704046502027511470502740806040032b9843790879150638020105055920450450060636928

>P1;d2aefa2
877a8666870687543270604-a05049323980606751504130035c-a447807-b150-4b030201046-30-70593054------


Translating the sequences
CC-HHHHHHHHHCCCEEEEEECC*CCCCCCCCHHHHCHHHHHCCEEEEEEEC*EEEECCC*CCCC*CCCEEEEEECH*HH*HHHHHHHC******
CC*HHHHHHHHHCCCEEEEEECC-CCCCCCCCHHHHCHHHHHCCEEEEEE*C-*EEECCC-CCCC-CCCEEEEEEC*-**-**HHHH*C------

116726.tem
_________________________________
CC-HHHHHHHHHCCCEEEEEECC-CCCCCCCCHHHHCHHHHHCCEEEEEEEC-EEEECCC-CCCC-CCCEEEEEECH-HH-HHHHHHHC------




Structural block scores
0	1	C	5.0	H	  6.5  7.5

3	11	H	5.0	H	  6.3  6.4

12	14	C	5.0	H	  8.2  6.7

15	20	E	5.0	H	  2.8  3.7

21	22	C	5.0	H	  2.0  2.0

24	31	C	5.0	H	  2.8  4.2

32	35	H	5.0	H	  3.0  5.0

37	41	H	5.0	H	  2.6  3.8

42	43	C	5.0	H	  4.0  2.5

44	50	E	4.7	H	  2.1  2.3

53	56	E	4.5	M	  5.5  6.4

57	59	C	5.0	H	  5.7  5.0

61	64	C	5.0	H	  3.8  4.4

66	68	C	5.0	H	  3.7  5.2

69	74	E	5.0	H	  1.3  1.0

78	79	H	3.0	P	  1.0  1.5

81	87	H	4.1	M	  2.9  4.1

89	94	-	3.0	P	  5.7  75.0

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