Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1m2oa1
CHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHC

>P1;d1pd0a1
CHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCCCHHHCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHC
PSA

>P1;d1m2oa1
815450072035008407967486026203522574177509479b58a34806882550241063036150055aa069a4077317303627574017203

>P1;d1pd0a1
82453036206400630573537402720660186216727855bc-b967314781750240062016130046a906aa6177108504716485027406


Translating the sequences
CHHHHHHHHHHHHHHH***CCHHHHHHHHHHHHHHHHHHH***CCC*HHHCCCC***CHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHH**CCHHHHHHHHC
CHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC-***CCCCHHHC*HHHHHHHHH*CCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHC

81811.tem
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CHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC-HHHCCCCHHHCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHC




Structural block scores
1	18	H	4.7	H	  3.3  3.1

19	20	C	5.0	H	  6.5  4.0

21	42	H	4.7	H	  4.0  4.1

43	45	C	5.0	H	  9.2  9.7

47	49	H	3.0	P	  7.2  8.8

50	53	C	5.0	H	  4.5  3.8

54	56	H	3.0	P	  6.0  5.3

58	68	H	4.6	H	  2.7  2.4

69	78	C	5.0	H	  4.3  4.0

79	91	H	4.7	H	  4.7  5.2

92	93	C	5.0	H	  4.5  3.5

94	101	H	5.0	H	  3.2  3.8

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