Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2ayda-
CEEEEEEECCCCCCCCCCCEEEEEEECCCCCCCCEEEEEECCC---CCCCEEEEEECCCCCCEEEEEEECCCCCCCCCC

>P1;d5w3xd-
------------CCCC-CCEEEEEEECCCCCCCCEEEEEECCHHHHCCCCEEEEECCCC---CCEEEEECCCCCC-CC-
PSA

>P1;d2ayda-
76735536299682a25250734747a1aa0753312160229---c05050202113a475202021538162b519b

>P1;d5w3xd-
------------8491-35064765892aa1624303230035a65807040221554a---62715464a0619-3b-


Translating the sequences
************CCCC*CCEEEEEEECCCCCCCCEEEEEECC*---CCCCEEEEEECCC***EEEEEEECCCCCC*CC*
------------CCCC-CCEEEEEEECCCCCCCCEEEEEECCH***CCCCEEEEE*CCC---**EEEEECCCCCC-CC-

118290.tem
_________________________________
------------CCCC-CCEEEEEEECCCCCCCCEEEEEECCH---CCCCEEEEEECCC---EEEEEEECCCCCC-CC-




Structural block scores
0	11	-	3.0	P	  5.7  75.0

12	15	C	5.0	H	  5.6  5.5

17	18	C	5.0	H	  3.5  4.0

19	25	E	5.0	H	  4.6  5.1

26	33	C	5.0	H	  5.9  5.6

34	39	E	5.0	H	  2.2  1.8

40	41	C	5.0	H	  2.0  1.5

43	45	-	3.0	P	  75.0  7.2

46	49	C	5.0	H	  4.4  3.8

50	55	E	4.7	H	  1.7  2.3

56	58	C	5.0	H	  4.8  6.5

59	61	-	3.0	P	  5.3  75.0

62	68	E	4.4	M	  1.7  4.4

69	74	C	5.0	H	  5.2  5.1

76	77	C	5.0	H	  5.0  7.2

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