Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1exka-
CCCCCCCCCCEEECHHHCCCCCCCCCCCEECHHHCCCCEEEEEE--CC-EEEEEE-CHHHCCCCEECC--CCCHHHCCCCEEECC

>P1;d1nlta3
---------CEEECCCCCCCCCCCC-CCCCCCCCCCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEC-
PSA

>P1;d1exka-
a7a989575645509509010055b3a14806608061614655--c8-808567-077041303107--250c40706014366

>P1;d1nlta3
---------773708707020077b-026a0a30a98022554767b86265445706704a40303398330720918333a6-


Translating the sequences
*********CEEECHHHCCCCCCCC*CCEECHHHCCCCEEEEEE--CC-EEEEEE-CHHHCCCCEECC--CCCHHHCCCCEEEC*
---------CEEEC***CCCCCCCC-CC**C***CCCC*EEEEE**CC*EEEEE**C***CCCC**CC**CCC***CCCCEEEC-

57938.tem
_________________________________
---------CEEECHHHCCCCCCCC-CCEECHHHCCCCEEEEEE--CC-EEEEEE-CHHHCCCCEECC--CCCHHHCCCCEEEC-




Structural block scores
0	8	-	3.0	P	  7.9  75.0

10	12	E	5.0	H	  4.7  5.7

14	16	H	3.0	P	  4.7  5.0

17	24	C	5.0	H	  3.9  4.3

26	27	C	5.0	H	  5.8  1.0

28	29	E	3.0	P	  6.0  8.2

31	33	H	3.0	P	  4.0  4.5

34	37	C	5.0	H	  3.8  6.9

38	43	E	4.7	H	  4.5  4.2

44	45	-	3.0	P	  75.0  6.5

46	47	C	5.0	H	  10.2  9.8

49	54	E	4.7	H	  5.7  4.3

57	59	H	3.0	P	  4.7  4.3

60	63	C	5.0	H	  2.0  4.6

64	65	E	3.0	P	  2.0  1.5

66	67	C	5.0	H	  3.5  3.0

68	69	-	3.0	P	  75.0  8.5

70	72	C	5.0	H	  2.3  2.0

73	75	H	3.0	P	  5.5  3.0

76	79	C	5.0	H	  3.2  5.2

80	82	E	5.0	H	  2.7  5.5

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