Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d6uxeb-
----------------CCCHHHHHHHHHHHHHHHHCCCC----CHHHHHHHHHHC-CCCC-CCCC-CHHHHHHHHC-CHHHHHHHHH----HHHHHHH----CCC-----CCCCCC--------

>P1;d6yj4w-
CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHCCCCCCCCCCCCCCCCCCHHHHHHCCCC-

>P1;d6zk9g-
C------CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHCCCCC----CCCCCCCCHHHHHHHCCCC
PSA

>P1;d6uxeb-
----------------b7758733581474026106514----638723713650-7428-56a2-6895357405-1587046167----5075736----849-----a75a61--------

>P1;d6yj4w-
aa9766523a6750b5595076145402541371044019309071546204811553235459395276205312651530140125517595028305736b89c9751978754774a71-

>P1;d6zk9g-
b------a593360762830563466026514810371194080a06485126115632664781942450063027356416405566175631263166----a799729896437657a89


Translating the sequences
----------------***HHHHHHHHHHHHHHHH****----C***HHHHHHH*-****-CCCC-CHHHHHHHH*-*HHHHHHHH*----HHHHH**----CCC-----CCC***--------
C******CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH*CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHH*CCCCC*CCCCCCCCCCCHHHHHH*CCC-
C------CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH*CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHCCCCC----CCCCCCCCHHHHHH*CCC*

418775.tem
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C------CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH*CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHCCCCC-CCCCCCCCCCCHHHHHH*CCC-




Structural block scores
1	6	-	4.0	M	  75.0  7.2  75.0

7	15	C	4.0	M	  75.0  5.6  5.5

16	40	H	4.6	H	  10.2  3.6  3.8

41	46	C	4.2	M	  29.0  3.7  4.1

47	59	H	4.5	M	  9.5  3.4  3.8

61	66	C	4.8	H	  17.4  5.8  5.5

67	85	H	4.8	H	  8.4  2.8  3.3

86	90	C	4.0	M	  61.4  4.0  5.0

91	95	H	4.8	H	  4.8  4.2  3.4

96	100	C	4.0	M	  46.8  4.6  4.4

102	112	C	4.3	M	  38.0  7.7  26.0

113	118	H	4.0	M	  40.4  6.3  5.8

120	122	C	4.0	M	  75.0  6.2  8.5

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