Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1j8ba-
--CCCCCCCCCCCCCCC-CCHHH-CEEEEEECCCCEEEEEECCCCEEEEEECCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC

>P1;d1ybxa-
----CCCCCCCCCCCCC--CCCC--EEEEEECCCCEEEEEECC-CC-CEEECHHHCCCCCCCCHHHHHHHHHHHHHHHHC-CHHHHHHHC-

>P1;d3f42a1
CHHHHHHHHHCCHHHHHHHHHHHCCEEEEECCCC-CEEEEECCCCEEEEECCHHHH--HCCCCCCCC-CHHHHHHHHHHHHHHHHHH-CCC
PSA

>P1;d1j8ba-
--85aa54975977768-68237-52140315a24050001073735637339618--98872583475046202650671386476899a

>P1;d1ybxa-
----c997876871850--9426--5360315d5002020414-92-837358725589768278238702640373068-386266627-

>P1;d3f42a1
9aa85899789878766438816976431620d4-020100222624637379827--968826743-5039605830656258379-898


Translating the sequences
--**CCCCCCCCCCCCC-*CHHH-CEEEEEECCCCEEEEEECCCCEEEEEEC***C--CCCCCHHHHHHHHHHHHHHHHHHHHH****CCC
----CCCCCCCCCCCCC--C***--EEEEEECCCCEEEEEECC-C*-*EEECHHHC**CCCCCHHHHHHHHHHHHHHHH*-*HHHHH**C-
**********CC********HHH*CEEEEE*CCC-*EEEEECCCCEEEEE*CHHH*--*CCCC****-*HHHHHHHHHHHHHHHHHH-CCC

82607.tem
_________________________________
--**CCCCCCCCCCCCC-*CHHH-CEEEEEECCCCEEEEEECCCCEEEEEECHHHC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHH*CCC




Structural block scores
0	1	-	4.0	M	  75.0  75.0  9.8

2	3	*	2.7	P	  6.5  75.0  9.2

4	16	C	4.2	M	  7.3  6.7  7.5

20	22	H	4.0	M	  4.0  4.0  5.0

25	30	E	4.8	H	  1.8  3.0  3.7

31	34	C	4.8	H	  5.4  5.9  23.1

35	40	E	4.8	H	  1.0  1.3  0.5

41	44	C	4.8	H	  4.2  22.2  3.0

45	50	E	4.3	M	  4.5  16.3  4.2

52	54	H	4.0	M	  5.3  5.7  6.3

56	57	-	4.0	M	  75.0  6.5  75.0

58	62	C	4.8	H	  6.8  6.4  6.6

63	86	H	4.5	M	  4.4  7.5  7.7

88	90	C	4.3	M	  9.5  28.0  8.3

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