Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1i3ja-
CCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCEEEC-----CEEECCHHHHHHHHCCCHHHHHHHHHCC-----CCCEEECC--

>P1;d1u3em2
------------------------------------CCCHHHHHHHH---HHCCCCEEEECCCCCEEEECCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCEEEECCCC
PSA

>P1;d1i3ja-
4607486819884a219925759b75485486947a83677656967c646ba4660006-----977170242006638187b40671182b-----9470524a--

>P1;d1u3em2
------------------------------------97776877549---77847403022577857406117400852a066b3053005975961572205339cf


Translating the sequences
************************************HHHHHHHHHH******CCCCEEE*-----*EEECCHHHHHHHHCCCHHHHHHHHHCC-----CC*EEECC--
------------------------------------***HHHHHHHH---HHCCCCEEEE*****EEEECCHHHHHHHHCCCHHHHHHHH*CC*****CCEEEECC**

64496.tem
_________________________________
------------------------------------HHHHHHHHHHH---HHCCCCEEEE-----EEEECCHHHHHHHHCCCHHHHHHHHHCC-----CCEEEECC--




Structural block scores
0	35	-	3.0	P	  6.2  75.0

36	46	H	4.3	M	  6.4  6.9

47	49	-	3.0	P	  7.5  75.0

50	51	H	3.0	P	  8.8  7.0

52	55	C	5.0	H	  6.6  5.8

56	59	E	4.5	M	  1.5  1.2

60	64	-	3.0	P	  75.0  5.8

65	68	E	4.5	M	  6.0  4.0

69	70	C	5.0	H	  3.5  3.5

71	78	H	5.0	H	  2.9  3.4

79	81	C	5.0	H	  5.7  5.5

82	90	H	4.8	H	  5.1  3.7

91	92	C	5.0	H	  6.8  8.0

93	97	-	3.0	P	  75.0  5.2

98	99	C	5.0	H	  6.5  4.5

100	103	E	4.5	M	  3.5  2.5

104	105	C	5.0	H	  7.2  6.0

106	107	-	3.0	P	  75.0  17.5

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