Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1nu9c1
CCCCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC---------------------------------------------------

>P1;d1nu9c2
------------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCCCHHHHHHHHHHHHHHHCCC---------------------------------CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC--------CCCCCCCCCCCHHHHCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHCCCCCC
PSA

>P1;d1nu9c1
9a77824931508890178a516784079227307621880482085b7177a507a026503310300531145115601571377176437666a2969357397071530046006102700640163067207724874a9---------------------------------------------------

>P1;d1nu9c2
------------------69719a75196047606510330100120-0152a81572045047404821279---------------------------------9756703186416511550410001002509--------22209a042156871378745a4057007604630891977048803492f


Translating the sequences
******************CCCCCHHHHHHHHHHHHHHHHHHHHHHH**HHCCHHHHHHHHHHHHHHHHHHHHH*********************************CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH********---------------------------------------------------
------------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHH-H*CC***HHHHHHHHHHHHHHH***---------------------------------CCCCCCCCHHHHHHHHHHHHHHHHHHHHHH*--------***************************************************

101094.tem
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------------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHHHHHHHHHHHH---------------------------------CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH-----------------------------------------------------------




Structural block scores
0	17	-	3.0	P	  5.5  75.0

18	22	C	5.0	H	  6.1  6.4

23	46	H	4.9	H	  4.5  3.2

48	49	H	4.0	M	  4.0  0.5

50	51	C	5.0	H	  7.0  3.5

52	72	H	4.4	M	  3.1  4.3

73	105	-	3.0	P	  4.9  75.0

106	113	C	5.0	H	  2.9  4.8

114	136	H	4.9	H	  3.0  2.8

137	195	-	3.0	P	  65.7  14.4

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