Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1ku3a-
--------------CCCCCCHHHHHHHHHHCCCCC--CCCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHHHC---------------

>P1;d1l0oc-
----------CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHC--CCHHHHHHHHHHHC---------------------

>P1;d1or7a1
CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHH--CC--C--CCHHHHHHHCC--CCHHHHHHHHHHHHHHHHHHHCC------------

>P1;d1rp3a1
-----------------------CCCCCCCCCCCCCCCCCCCHHHHCC-CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHCC

>P1;d4g7hf2
------------CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHCC---CCCCCC------------
PSA

>P1;d1ku3a-
--------------389606a70340040230645--96806175008629--48364047105604732983---------------

>P1;d1l0oc-
----------d967897436710740650564038548680566100840b--25395076066217---------------------

>P1;d1or7a1
c959976376424711870685223003034--56--6--2738601851a--17694076205604541497386------------

>P1;d1rp3a1
-----------------------9917317a230b72a5806574106-2c393606149708626667758575664686687595c

>P1;d4g7hf2
------------8824974573175066127814873a58064730083069a16274066147617---96a7a9------------


Translating the sequences
--------------C*****HHHHHHHHHH***CC--CCCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHHH*---------------
----------****C*HH**HHHHHHHHHHH******CCCCCHHHHHHHHC--CCHHHHHHHHHHH*---------------------
****************HH**HHHHHHHHHHH--CC--C--CCHHHHHHH*C--CCHHHHHHHHHHHHHHHHH****------------
-----------------------**********CC**CCCCCHHHH**-*C**CC***HHHHHHHHHHHHHH****************
------------**C*HH**HHHHHHHHHHH******CCCCCHHHHHHHHC**CCHHHHHHHHHH**---******------------

88659.tem
_________________________________
------------**C*HH**HHHHHHHHHHH**CC**CCCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHHH****------------




Structural block scores
0	11	-	4.4	M	  75.0  64.4  6.6  75.0  75.0

12	13	*	3.0	P	  75.0  6.5  5.5  75.0  8.0

16	17	H	4.1	M	  7.5  5.5  7.5  75.0  8.0

18	19	*	2.1	P	  3.0  4.5  3.0  75.0  4.5

20	30	H	4.4	M	  3.0  3.7  2.7  24.8  4.1

31	32	*	2.1	P	  3.0  2.0  75.0  2.5  4.5

33	34	C	3.8	M	  4.5  5.5  5.5  5.8  6.0

35	36	*	3.0	P	  75.0  4.5  75.0  4.5  5.0

37	41	C	4.8	H	  5.8  5.4  33.0  5.9  5.9

42	49	H	4.7	H	  3.6  3.1  4.0  12.5  3.1

51	52	-	3.8	M	  75.0  75.0  75.0  6.0  9.8

53	54	C	5.0	H	  6.0  3.5  4.0  4.5  3.5

55	71	H	4.6	H	  4.1  25.1  4.2  5.2  17.1

72	75	*	2.8	P	  57.0  75.0  6.0  5.8  9.2

76	87	-	4.5	M	  75.0  75.0  75.0  6.9  75.0

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