Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1en2a1
--CCCCCCCCCCCHHHCEEECCCCEECCHHHHC-CCEEECCHHHCCC

>P1;d1p9ga-
--CHHHHC-CCCCCCCCEEECCCCEECCHHHHCCCCEEECCCC----

>P1;d1uhaa1
CCCCCHHHCCCCCHHHCEECCCCCEECCHHHHC-CCCCCCCCC----
PSA

>P1;d1en2a1
--403860b76408b650005606246655302-82036526a99ac

>P1;d1p9ga-
--b05852-9500b8930003738126a98326ab505203a3----

>P1;d1uhaa1
93502871a87707a7400158051237aa316-a402323b5----


Translating the sequences
--CCC**CCCCCCHHHCEEECCCCEECCHHHHC-CCEEECC******
--C**HHC-CCCC***CEEECCCCEECCHHHHC*CCEEECCCC----
**CCCHH*CCCCCHHHCEE*CCCCEECCHHHHC-CC***CCCC----

57016.tem
_________________________________
--CCCHHCCCCCCHHHCEEECCCCEECCHHHHC-CCEEECCCC----




Structural block scores
0	1	-	4.0	M	  75.0  75.0  6.0

2	4	C	4.3	M	  2.3  5.5  2.3

5	6	H	4.0	M	  7.0  6.5  7.5

7	12	C	4.7	H	  4.8  15.2  5.6

13	15	H	4.0	M	  8.5  9.5  8.2

17	19	E	4.7	H	  0.0  0.0  0.3

20	23	C	5.0	H	  4.2  5.2  4.5

24	25	E	5.0	H	  3.0  1.5  1.5

26	27	C	5.0	H	  6.0  8.2  5.0

28	31	H	5.0	H	  3.2  5.5  6.2

34	35	C	5.0	H	  5.0  8.2  7.2

36	38	E	4.0	M	  3.0  2.3  1.7

39	42	C	4.5	M	  5.9  4.1  5.4

43	46	-	4.0	M	  10.2  75.0  75.0

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