Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1k8ba-
---------------------------------CEEEECCEEEECCHHHHHHHHHCCHHHHHHHHHHHHCCEEEEECCEEEEECC----------------

>P1;d2d74b1
CCCCCHHHHHHCCCCCCCHHHHCCCCCCCCCCCCEEEECCEEEECCHHHHHHHHCCCCHHHHHHHHHHCCCCEEEECCEEEECCCCCHHHHHHHHHHHHHC
PSA

>P1;d1k8ba-
---------------------------------85785ca5050856a8049259961563045037737150835706000384----------------

>P1;d2d74b1
4799488733965686434041689237814b050428c940003103400610a575770071026209180748b650307661749404411340166


Translating the sequences
---------------------------------CEEEECCEEEECCHHHHHHHHHCCHHHHHHHHHHHHCCEEEEECCEEEEECC----------------
*********************************CEEEECCEEEECCHHHHHHHH*CC*HHHHHHHHHH*CC*EEEECCEEEE*CC****************

100966.tem
_________________________________
---------------------------------CEEEECCEEEECCHHHHHHHHHCCHHHHHHHHHHHHCCEEEEECCEEEEECC----------------




Structural block scores
0	32	-	3.0	P	  75.0  5.4

34	37	E	5.0	H	  6.2  3.5

38	39	C	5.0	H	  11.5  10.8

40	43	E	5.0	H	  2.5  1.0

44	45	C	5.0	H	  6.5  2.0

46	54	H	4.8	H	  5.9  2.7

55	56	C	5.0	H	  7.5  6.0

57	68	H	4.7	H	  3.7  3.1

69	70	C	5.0	H	  4.0  5.0

71	75	E	4.6	H	  4.2  5.4

76	77	C	5.0	H	  3.5  8.8

78	82	E	4.6	H	  1.8  3.0

83	84	C	5.0	H	  6.0  6.0

85	100	-	3.0	P	  75.0  3.4

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