Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1azta1
-----CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCC--------CCCCCHHHHHHHHHHHHCHHHHHHHHCHHHCCCCCCHHHHHCCHHHHHCCCCCCCHHHHHHCC---

>P1;d1cipa1
CCHHHHHHCHHHHHHHHHHHHHHHHHHHHHH--CCCCCCCCHHHHHHHHHHHHH---HHHHCCCC----HHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHCCHHHHCCCCCCCCHHHHHCCCCCC

>P1;d1zcba1
CCHHHHHCCHHHHHHHHHHHHHHHHHHHHHC--CCCCCCHHHHHHHHHHHCCCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHCCHHHHCCCCCCCCHHHHHHCCC--
PSA

>P1;d1azta1
-----6a8526402600140012003108809841804689166216204723a39--------b1a0286006104200608104502722a41a01b00420052056036ba0707a5037417---

>P1;d1cipa1
4669604832430031007002301800b51--919237a8158117405721a---40472807----a6004003400708103602743a41a01b103200740930078b03066500740578b

>P1;d1zcba1
5968322732200001003002400401672--908026a9158307402808395940576206294037106004200807005601744a52a07a00430053084005890405860073076--


Translating the sequences
-----*HH*HHHHHHHHHHHHHHHHHHH**C**CCCCCCHHHHHHHHHHHHCCCCC--------C****HHHHHHHHHHHHCHHHHHHHH*HHHCCCCCCHHHHHCCHHHH*CCCCCCCHHHHHHCC---
CCHHHHHHCHHHHHHHHHHHHHHHHHHHHH*--CCCCCC**HHHHHHHHHH***---HHH*CCCC----HHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHCCHHHHCCCCCCCCHHHHH*CCC**
CCHHHHH*CHHHHHHHHHHHHHHHHHHHHHC--CCCCCCHHHHHHHHHHH*CCCCC*HHH*CCCC****HHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHCCHHHHCCCCCCCCHHHHHHCCC--

47895.tem
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CCHHHHHHCHHHHHHHHHHHHHHHHHHHHHC--CCCCCCHHHHHHHHHHHHCCCCC-HHH*CCCC****HHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHCCHHHHCCCCCCCCHHHHHHCCC--




Structural block scores
0	1	C	4.0	M	  75.0  5.0  7.0

2	7	H	4.2	M	  41.6  5.5  4.7

9	29	H	4.9	H	  2.3  2.4  1.5

31	32	-	4.0	M	  8.5  75.0  75.0

33	38	C	5.0	H	  3.8  5.2  4.2

39	50	H	4.8	H	  4.3  4.8  4.8

51	55	C	4.0	M	  5.5  32.7  5.0

57	59	H	4.0	M	  75.0  2.7  3.0

61	64	C	4.2	M	  59.1  4.2  3.5

65	68	*	2.7	P	  3.4  75.0  3.8

69	80	H	5.0	H	  2.8  2.9  2.6

82	93	H	4.9	H	  3.8  4.0  4.1

94	99	C	5.0	H	  4.0  4.2  5.0

100	104	H	5.0	H	  1.2  1.0  1.4

105	106	C	5.0	H	  3.5  5.5  4.0

107	110	H	5.0	H	  2.8  3.0  3.0

111	118	C	4.9	H	  5.6  4.4  3.9

119	124	H	4.8	H	  4.9  3.7  4.0

125	127	C	4.7	H	  27.7  4.0  4.3

128	129	-	4.0	M	  75.0  9.8  75.0

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