Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2fj8a1
CCCCCCCEEECCCCCCEEEECCCCC-CCCCCCCCEEECCCCCCCEEECCCEECCCCCCCC

>P1;d2g81i1
--CCCCCEEECCCCCCCEEECCEEECCCCCCCCCEEECCCCCCEEEECCCCC-CCCCCC-
PSA

>P1;d2fj8a1
01920361517a7b30405041248-902980942650a957a24205266718606739

>P1;d2g81i1
--420571726a69735050415367600830972636a6a52605042546-532782-


Translating the sequences
**CCCCCEEECCCCCCEEEECC***-CCCCCCCCEEECCCCCC*EEECCCEE*CCCCCC*
--CCCCCEEECCCCCC*EEECCEEE*CCCCCCCCEEECCCCCCEEEECCC**-CCCCCC-

57247.tem
_________________________________
--CCCCCEEECCCCCCEEEECCEEE-CCCCCCCCEEECCCCCCEEEECCCEE-CCCCCC-




Structural block scores
0	1	-	3.0	P	  0.5  75.0

2	6	C	5.0	H	  4.0  3.6

7	9	E	5.0	H	  2.3  3.3

10	15	C	5.0	H	  6.5  6.9

16	19	E	4.5	M	  2.2  2.5

20	21	C	5.0	H	  2.5  2.5

22	24	E	3.0	P	  4.7  4.7

26	33	C	5.0	H	  5.1  4.1

34	36	E	5.0	H	  4.3  3.7

37	42	C	5.0	H	  7.0  6.7

43	46	E	4.5	M	  2.0  2.8

47	49	C	5.0	H	  4.3  3.7

50	51	E	3.0	P	  6.5  5.0

53	58	C	5.0	H	  5.0  4.5

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