Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1j3ma-
---CEEEEECCCHHHHHHHHHHHHHHCCCEEEEEEEHHHHHHHHHCCCCCCEEEEEEECHHHHHHHHHHCHHHHHHCCEEEEEEEECCEEEEEECCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHC-

>P1;d1q9ua-
CCCEEEEECCCCHHHHHHHHHHHHHHCCCCCCEEEEHHHHHHHCCCCCCCCEEEEEC-CHHHHHHHHHHCHHHHHHCC-CEEEEEECCEEEEEEECHHHHHHCCC---CHHHHHHHHHHHHHHHHHHHCCC
PSA

>P1;d1j3ma-
---8053209083a602850570086170905736522654678684956441200010790175049626705912214010353a8501020201463077178632670661064136303601731-

>P1;d1q9ua-
97733106092a1a501740461077280a1763342165347796b3833212010-17814750393396048233-4020235a84020102212430361b---28605820461182023003506


Translating the sequences
---*EEEEECCCHHHHHHHHHHHHHHCCCEEEEEEEHHHHHHHHHCCCCCCEEEEEE*CHHHHHHHHHHCHHHHHHCC*EEEEEEECCEEEEEE*CHHHHHHHCC***HHHHHHHHHHHHHHHHHHHHHC-
***EEEEE*CCCHHHHHHHHHHHHHHCCC***EEEEHHHHHHH**CCCCCCEEEEE*-CHHHHHHHHHHCHHHHHHCC-*EEEEEECCEEEEEEECHHHHHH*CC---*HHHHHHHHHHHHHHHHHHH*C*

103247.tem
_________________________________
---EEEEEECCCHHHHHHHHHHHHHHCCCEEEEEEEHHHHHHHHHCCCCCCEEEEEE-CHHHHHHHHHHCHHHHHHCC-EEEEEEECCEEEEEEECHHHHHHHCC---HHHHHHHHHHHHHHHHHHHHHC-




Structural block scores
0	2	-	3.0	P	  75.0  7.7

3	8	E	4.3	M	  3.0  2.2

9	11	C	5.0	H	  5.7  7.2

12	25	H	5.0	H	  4.3  3.8

26	28	C	5.0	H	  2.7  3.3

29	35	E	4.1	M	  5.0  4.9

36	44	H	4.6	H	  5.1  4.9

45	50	C	5.0	H	  6.0  5.8

51	56	E	4.7	H	  1.2  1.0

59	68	H	5.0	H	  4.8  4.7

70	75	H	5.0	H	  4.7  4.8

76	77	C	5.0	H	  2.0  3.0

79	85	E	4.7	H	  2.3  2.3

86	87	C	5.0	H	  9.2  9.2

88	94	E	4.7	H	  1.4  1.3

96	102	H	4.7	H	  4.0  2.7

103	104	C	5.0	H	  4.0  6.2

105	107	-	3.0	P	  5.7  75.0

108	128	H	4.8	H	  3.4  3.1

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