Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1frea-
-----------CCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCC--------------------

>P1;d2csva1
CCCCCCCCCCCCCCCCCC-CCCCEEECCCC-CEECHHHHCC-CCCCCCEEEHHHHHHHHCC----------C

>P1;d2d8va1
----------CCCCCCCCC-CCCEEECCCCCEEECCCHHHH-HCCCC------CCCCCCCCCCCCCCCCCCC

>P1;d2dida1
----------CCCCCCCC-CCCCEEECCCC-CEECHHHHCCCCCCCCCEEEC--------------------

>P1;d2djaa1
CCCCCCCCCCCCCCCCCCCCCCCEEEHHHC-EEECHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

>P1;d3ddta1
--------CCCCCCCCCCCCCCCEEECCCC-EEECHHHHHHCCCCCCCEEECCC------------------

>P1;d5k3qa-
----------CCCCCCCC-CCCCEEECCCC-EEECHHHHHC-CCC--CCEECCC------------------
PSA

>P1;d1frea-
-----------2706a11b8222216a5--c7a83410663690a947043a--------------------

>P1;d2csva1
aba788986588407726-53161105647-5500450259-315c47036386357a77a----------a

>P1;d2d8va1
----------744056338-605350663a12101770176-81787------6178181683718868b9c

>P1;d2dida1
----------86607937-44141205637-5300551173a607a361374--------------------

>P1;d2djaa1
e78b74b59686105523256171306467-56004403682816a392684d8a9799a8b7945a1ca8a

>P1;d3ddta1
--------ea4740a728a36151404647-55004403674907a1814638b------------------

>P1;d5k3qa-
----------2950b528-35111407647-6400630473-70e--306745b------------------


Translating the sequences
-----------CCCCCCC*CCCC***CC--****C*******CCCCCC***C--------------------
**********CCCCCCCC-CCCCEEECCCC-*EECHHHH**-CCCCCC*************----------*
----------CCCCCCCC*-CCCEEECCCC**EEC**HH**-*CCCC------*******************
----------CCCCCCCC-CCCCEEECCCC-*EECHHHH***CCCCCC***C--------------------
**********CCCCCCCC*CCCCEEE***C-*EECHHHH***CCCCCC***C********************
--------**CCCCCCCC*CCCCEEECCCC-*EECHHHH***CCCCCC***C**------------------
----------CCCCCCCC-CCCCEEECCCC-*EECHHHH**-CCC--C***C**------------------

57845.tem
_________________________________
--------**CCCCCCCC*CCCCEEECCCC-*EECHHHH***CCCCCC***C*********----------*




Structural block scores
0	7	-	4.2	M	  75.0  9.1  75.0  75.0  8.6  75.0  75.0

8	9	*	3.7	M	  75.0  5.5  75.0  75.0  7.5  12.5  75.0

10	17	C	5.0	H	  12.8  5.2  4.0  5.8  3.8  5.3  5.3

19	22	C	4.9	H	  3.5  3.8  21.5  3.2  4.8  3.8  2.5

23	25	E	4.6	H	  3.0  0.7  2.7  1.0  1.3  1.7  1.7

26	29	C	4.5	M	  41.4  5.5  6.4  5.2  5.8  5.2  6.0

32	33	E	4.6	H	  9.2  2.5  0.5  1.5  3.0  2.5  2.0

35	38	H	4.4	M	  2.8  2.8  3.8  3.0  2.8  2.8  3.2

39	41	*	1.7	P	  5.0  29.7  29.3  6.8  5.3  5.7  28.3

42	47	C	4.7	H	  6.6  5.4  17.7  5.4  6.2  5.9  29.1

48	50	*	1.8	P	  2.3  3.0  75.0  3.7  5.3  3.7  4.3

52	60	*	3.5	M	  75.0  7.1  12.6  75.0  9.4  60.5  60.2

61	70	-	4.2	M	  75.0  75.0  7.0  75.0  7.9  75.0  75.0

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