Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1g9la1
-----------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCHHHHHHHC--CCCCCCHHHHCCCCCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCCCC

>P1;d1i2ta-
-----------------------------------------------------------------------CHHHHHHHHHHHHHHHC--HHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHC------------------

>P1;d1ifwa1
----------CCCCCC------------------------------------------CCCCC-----CCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCC--------C

>P1;d1nmra1
---------CCCCCCC------------------------------------------HHHHHHCCCHHHHHHHHHHHHHHHHHHCCC--CCCHHHHHHHCC--CCHHHHHHCCCCC--HHHHHHHHHHHHHHHHCCCCC------------

>P1;d6h7aa1
CCCCCHHHHH--------------------------------------------------HCC-----HHHHHHHHHHHHHHHHHCCC--CCCHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHCCC----------------C
PSA

>P1;d1g9la1
-----------aa49788386379a5b943878476a87ab5b998a887977aa893010630671468357610064045305500--67408300400170998127501725800651056017607677a49879a6a79aa3a7be

>P1;d1i2ta-
-----------------------------------------------------------------------75861088044304813--684086007202836794055018448305820660186278af------------------

>P1;d1ifwa1
----------b9daa8------------------------------------------d8988-----97932a53285036301774a496004401340792448702600548a70793287049316743783ab49aa--------e

>P1;d1nmra1
---------aca98ab------------------------------------------878889677875883950485049105763--680083038406--3a9008509936a--660273018204635c59a7c------------

>P1;d6h7aa1
5780659607--------------------------------------------------816-----8a615820162045405831--5a406601620172746401600746740453075037418776a----------------a


Translating the sequences
-----------CCCCC********************************************H*******************HHHHHHHC--CCC***HHHH*CCCC*HHHHH**CC**HHHHHHHHHHHHHH**C*C***C***********C
-----------------------------------------------------------------------*HHHHHHHHHHHHHHHC--***HHHHHHHHCCCCHHHHHHHH*CHHHHHHHHHHHHHHHHHHC------------------
----------*CCCCC------------------------------------------*****-----**HHHHHHHHHHHHHHHHHC**CCCHHHHHHHH**CCHHHHHHHHCCHHHHHHHHHHHHHHHHHH**C***C***--------C
---------**CCCCC------------------------------------------**H*********HHHHHHHHHHHHHHH**C--CCCHHHHHHH*C--C*HHHHHH*CC**--HHHHHHHHHHHHHH**C***C------------
**********--------------------------------------------------H**-----**HHHHHHHHHHHHHHH**C--CCCHHHHHHHHCCCCHHHHHHHH*CHHHHHHHHHHHHHHHHH*C*----------------C

63570.tem
_________________________________
-----------CCCCC------------------------------------------**H**-----**HHHHHHHHHHHHHHHHHC--CCCHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHC*C***C-----------C




Structural block scores
0	10	-	4.4	M	  75.0  75.0  69.2  63.5  11.6

11	15	C	4.2	M	  8.2  75.0  10.3  9.9  75.0

16	57	-	4.5	M	  7.7  75.0  75.0  75.0  75.0

58	59	*	3.0	P	  0.5  75.0  10.8  7.5  75.0

61	62	*	2.1	P	  4.5  75.0  8.0  8.0  3.5

63	67	-	3.8	M	  3.6  75.0  75.0  7.4  75.0

68	69	*	2.1	P	  7.0  75.0  8.0  6.0  9.2

70	86	H	4.5	M	  3.2  8.4  4.4  4.8  3.5

88	89	-	4.5	M	  75.0  75.0  7.2  75.0  75.0

90	92	C	4.5	M	  5.7  6.0  5.0  4.7  6.5

93	100	H	4.7	H	  1.9  2.9  2.0  3.2  2.6

101	104	C	4.5	M	  4.2  4.8  5.5  39.8  4.2

105	112	H	4.6	H	  4.1  3.9  3.4  5.2  2.6

113	114	C	4.4	M	  4.5  6.0  4.5  6.0  5.5

115	132	H	4.7	H	  3.9  4.7  5.3  11.9  4.3

136	138	*	3.0	P	  8.0  75.0  8.3  8.8  75.0

140	150	-	4.3	M	  8.7  75.0  57.3  75.0  75.0

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