Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1u9da1
--CEEEECCCCHHHHHHHHHHHHHHHHHHHCCCHHHCEEEECCCCCCCCCC-CCCCEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCHHHCEECCEEC

>P1;d3t5sa1
CCEEEEEECCCCCHHHHHHHHHC-CCCCC---CHHHCEEEEEECCCCCCCCCCCCEEEEEEC-----CC--CHHHHHHHCCCCCHH-HEEEEEC--------------
PSA

>P1;d1u9da1
--13030310648207603560275008309375b406152186a395ab9-250020102448772355036102610383389926080604738676357b9844

>P1;d3t5sa1
911020201129a7276029601-4036a---788607050653a253bb58830040225e-----98--497028105300758-1070334--------------


Translating the sequences
--*EEEE*CCCHHHHHHHHHHHH*HHHHH***CHHHCEEEE**CCCCCCCC-CCC*EEEE*C*****HH**HHHHHHHHHHHHC*******EEE**************
**EEEEEECCC**HHHHHHHHH*-*****---CHHHCEEEEEECCCCCCCC*CCCEEEEEEC-----**--*HHHHHHH****CHH-HEEEEE*--------------

55331-3.tem
_________________________________
--EEEEEECCCHHHHHHHHHHHH-HHHHH---CHHHCEEEEEECCCCCCCC-CCCEEEEEEC-----HH--HHHHHHHHHHHHCHH-HEEEEEE--------------




Structural block scores
0	1	-	3.0	P	  75.0  5.0

2	7	E	4.3	M	  1.7  0.8

8	10	C	5.0	H	  2.3  1.3

11	22	H	4.5	M	  3.6  5.0

24	28	H	3.0	P	  3.2  4.7

29	31	-	3.0	P	  4.0  75.0

33	35	H	5.0	H	  6.8  7.3

37	42	E	4.3	M	  3.8  3.8

43	50	C	5.0	H	  8.1  6.4

52	54	C	5.0	H	  2.3  3.7

55	60	E	4.3	M	  0.8  2.2

62	66	-	3.0	P	  5.6  75.0

67	68	H	3.0	P	  4.0  8.5

69	70	-	3.0	P	  2.5  75.0

71	82	H	4.2	M	  3.0  3.2

84	85	H	3.0	P	  9.0  6.5

88	93	E	3.7	M	  3.0  2.8

94	107	-	3.0	P	  6.3  75.0

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