Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1uoua3
CCCEEEEEECCCCEEEEEECHHHHHHHHHHHHC--------CCCCCEEEECCCCCCEE-CCCEEEEEEECCCCCCHHHHHHHHHHEEEECCCCCCCCCCCCCCCCCC

>P1;d3h5qa3
CCCEEEEEECCCCEEEEEECHHHHHHHC--CCCCCCCCCCCCCCCCEEEECCCCCCEECCCCEEEEEEECCCC-CHHHHHHHHHHEEEEC--CCCCCCCCCCCCCC-

>P1;d4eada3
CCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCCCCCCCCCCCCCCEEECCCCCCCEECCCCCCEEEEECCHHHHHHHHHHHHHHEEEEC-CCCCCCCCCCCCCCC-
PSA

>P1;d1uoua3
90655341505760002505a821770296136--------84920604420840550-754300302037870676137402800313a6953a369889789789

>P1;d3h5qa3
907343405076442015049b319702--0627496aa4a24930206241630560677520010203688-07a137403700505a--5497679687869d-

>P1;d4eada3
a072342050888230161789409403220403468a8491383020673085225049951002020456b10670184036007159-842aa65a877875d-


Translating the sequences
CCCEEEEEECCCCEEEEEECHHHHHHHHHH**C--------CCCCCEEEECCCCCCEE-CCCEEEEEEECCCC*CHHHHHHHHHHEEEEC*CCCCCCCCCCCCCCC*
CCCEEEEEECCCCEEEEEECHHHHHHH*--CCCCCCCCCCCCCCCCEEEECCCCCCEECCCCEEEEEEECCCC-CHHHHHHHHHHEEEEC--CCCCCCCCCCCCCC-
CCCEEEEE*CCCCEEEEEECHHHHHHHHHHCCCCCCCCCCCCCCCCEEE*CCCCCCEECCCC**EEEEECC****HHHHHHHHHHEEEEC-CCCCCCCCCCCCCCC-

54680.tem
_________________________________
CCCEEEEEECCCCEEEEEECHHHHHHHHHHCCCCCCCCCCCCCCCCEEEECCCCCCEECCCCEEEEEEECCCC*CHHHHHHHHHHEEEEC-CCCCCCCCCCCCCCC-




Structural block scores
0	2	C	5.0	H	  5.0  5.3  5.8

3	8	E	4.8	H	  3.8  3.2  2.7

9	12	C	5.0	H	  4.5  4.2  6.0

13	18	E	5.0	H	  1.2  2.0  2.2

20	29	H	4.7	H	  5.2  19.2  4.1

30	45	C	4.4	M	  39.6  5.5  4.5

46	49	E	4.8	H	  3.5  2.5  3.8

50	55	C	5.0	H	  3.2  3.2  3.3

56	57	E	5.0	H	  2.5  3.0  2.5

58	61	C	4.8	H	  22.8  6.2  6.8

62	68	E	4.7	H	  1.1  0.7  0.7

69	72	C	4.5	M	  6.2  6.2  6.6

75	84	H	5.0	H	  3.8  4.2  3.5

85	88	E	5.0	H	  1.8  2.5  3.2

91	105	C	4.9	H	  7.3  12.0  7.5

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