Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1eeja2
CHHHHHHHHHHCCCCEEEEEECCCCCEEEEEECC----EEEEEECCCCCEEECCCCCCCCCCCC

>P1;d1t3ba2
-CCCCCCC---------CCCC---CCCCCCCCC-----CCCCCCC---CCCCCCCCC--CCCCC

>P1;d1v58a2
CCCHHHHHHHCCCEEEEEEEECC-CCCEEEEEEECCEEEEEEECCCCCCEEECCCCCCC---CC
PSA

>P1;d1eeja2
977206810783a18165167065b813305055----8401024607726907266799b768

>P1;d1t3ba2
-6bb032a---------9308---b83130503-----8601061---a36797549--7d65a

>P1;d1v58a2
82392047137890915653b07-cb160030448a661201115658706357376b9---79


Translating the sequences
C**HHHHHHH*CC**EEEEEECC*CC*EEEEEC*----EEEEE*CCCCCEEECCCCCCCCCCCC
-CC*****---------****---CCC*****C-----*****CC---C***CCCCC--CCCCC
CCCHHHHHHH*CC**EEEEEECC-CCCEEEEE******EEEEECCCCCCEEECCCCCCC---CC

54423.tem
_________________________________
CCCHHHHHHH*CC**EEEEEECC-CCCEEEEEC*----EEEEECCCCCCEEECCCCCCCCCCCC




Structural block scores
0	2	C	4.0	M	  7.7  30.8  4.3

3	9	H	4.0	M	  3.4  25.3  3.7

11	12	C	4.0	M	  6.8  75.0  8.5

13	14	*	2.7	P	  4.5  75.0  4.5

15	20	E	4.0	M	  4.3  28.3  5.2

21	22	C	4.0	M	  3.0  75.0  3.5

24	26	C	4.7	H	  6.8  7.5  8.3

27	31	E	4.0	M	  2.2  1.8  1.8

34	37	-	4.0	M	  75.0  75.0  7.6

38	42	E	4.0	M	  2.6  3.0  1.0

43	48	C	4.3	M	  4.3  40.4  5.3

49	51	E	4.0	M	  5.7  5.3  3.0

52	63	C	4.6	H	  6.5  18.8  24.1

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