Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2bh1x1
------------------------------------------------------------------------CCCCCHHHHHHHCEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHCC

>P1;d2d28c1
CCCCHHHHHHHHHHHCCCCCHHHHHHCCCCCHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCHHHCCCCCCCCCCCCCHHHHHHHCEEEEEEECC-EEEEEECCCCCHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHCC
PSA

>P1;d2bh1x1
------------------------------------------------------------------------4760668205743000215b756701011149257a01840773084a16345178960562186109

>P1;d2d28c1
ba572364015203758107881286069fa307206939107463104000512a254134950a9834a517707371045130011447bb-5000000201498015306a4092604110012620480064047


Translating the sequences
------------------------------------------------------------------------CCCCCHHHHHHHCEEEEE**CC**EEEEECCCCCHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHCC
************************************************************************CCCCCHHHHHHHCEEEEEEECC-EEEEEECCCCCHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHCC

160246.tem
_________________________________
------------------------------------------------------------------------CCCCCHHHHHHHCEEEEEEECC-EEEEEECCCCCHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHCC




Structural block scores
0	71	-	3.0	P	  75.0  4.7

72	76	C	5.0	H	  4.6  4.4

77	83	H	5.0	H	  4.6  3.0

85	91	E	4.4	M	  2.8  2.4

92	93	C	5.0	H	  6.0  11.5

95	100	E	4.7	H	  1.7  0.8

101	105	C	5.0	H	  4.2  1.4

106	116	H	5.0	H	  4.3  4.2

117	119	C	5.0	H	  7.5  5.7

120	124	E	5.0	H	  3.8  1.2

125	126	C	5.0	H	  4.0  0.5

127	137	H	5.0	H	  4.7  2.9

138	139	C	5.0	H	  4.5  5.5

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