Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2b7ea1
----------CHHHHHHHHHHHC--CCCCCCCHHHHHHHHHHHCCHHHHCC-CCHHHHHHHHHHHHHCC-----------

>P1;d2cqna1
--------CHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHC-CCHHHHHCC--CHHHHHHHHHHHHHHHHHHCCC-----

>P1;d2doea1
CCCCCCCCHHHHHHHHHHHHHHC--CCCCCCCHHHHHHHHC-CCHHHHCCC--CHHHHHHHHHHHHHHHHHCCCC-----

>P1;d2dofa1
CCCHHHCHHHHHHHHHHHHHHHHCC--CCCCCHHHHHHHHH-HCCCHHHHCCCCHHHHHHHHHHHHHHHHHHHHC-----

>P1;d2kisa1
--------CHHHHHHHHHHHHHH--CCCCCCCHHHHHHHHH-CCHHHHCCC---CCHHHHHHHHHHHHHHHHHHHCCCCC

>P1;d2l9va-
-----CCCHHHHHHHHHHHHHHC--CCCCCCCHHHHHHHHH-CCHHHHHHHCHHHHC-----------------------
PSA

>P1;d2b7ea1
----------9237401400451--a045b08185067500941710542a-655830450063128a6-----------

>P1;d2cqna1
--------989525603500691866086a27076037403-847107408--7893146007401663457698-----

>P1;d2doea1
a9859a55994157402700382--a066a06188047705-92750730a--669423600663178348b9ab-----

>P1;d2dofa1
8a877a4864503850470037307--61a37274037405-719618707507864036107711872566886-----

>P1;d2kisa1
--------5a8326502600541--7030636386037203-617318207---871163025702662265366786c9

>P1;d2l9va-
-----2d5985277036404853--907ad18875026204-807712740439759-----------------------


Translating the sequences
----------*HHHHHHHHHHHC--CCCCCCCHHHHHHHHH**C*HHHHCC-*CHHHHHHHHHHHHH**-----------
--------*HHHHHHHHHHHH*C**CCCCCCCHHHHHHHH*-CCHHHHHCC--CHHHHHHHHHHHHHHHHH****-----
*********HHHHHHHHHHHHHC--CCCCCCCHHHHHHHH*-CCHHHH*CC--CHHHHHHHHHHHHHHHHH****-----
*********HHHHHHHHHHHHH***--CCCCCHHHHHHHHH-*C**HHH*C**CHHHHHHHHHHHHHHHHH****-----
--------*HHHHHHHHHHHHH*--CCCCCCCHHHHHHHHH-CCHHHH*CC---**HHHHHHHHHHHHHHH*********
-----****HHHHHHHHHHHHHC--CCCCCCCHHHHHHHHH-CCHHHHH*****HH*-----------------------

81698.tem
_________________________________
-----****HHHHHHHHHHHHHC--CCCCCCCHHHHHHHHH-CCHHHHHCC-*CHHHHHHHHHHHHHHHHH****-----




Structural block scores
0	4	-	4.1	M	  75.0  75.0  8.3  8.1  75.0  75.0

5	8	*	3.0	P	  75.0  58.5  7.4  7.1  57.5  7.4

9	21	H	4.9	H	  8.8  4.5  3.8  3.5  4.0  4.5

23	24	-	4.1	M	  75.0  7.0  75.0  3.5  75.0  75.0

25	31	C	4.9	H	  5.6  5.6  5.6  25.4  3.6  7.0

32	40	H	4.9	H	  3.6  3.3  4.4  3.6  3.6  3.8

42	43	C	4.5	M	  2.5  6.0  5.5  4.0  3.5  4.0

44	48	H	4.5	M	  3.4  3.8  4.4  6.2  4.2  4.8

49	50	C	4.3	M	  6.2  4.0  5.2  3.5  3.5  2.0

54	70	H	4.4	M	  12.4  3.9  4.5  4.2  3.8  63.0

71	74	*	2.7	P	  75.0  7.5  10.6  7.0  5.0  75.0

75	79	-	4.5	M	  75.0  75.0  75.0  75.0  8.5  75.0

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