Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1f7ua3
CHHHHHHHHHHHCCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHCEECCCHHHCCEEEEHHHHCCC-CCCHHHHHHHHHHCCCCCCCEEEEEEECCEEEEEECHHHHHHHHHHHHHHHHHHCC

>P1;d1iq0a3
----------------------------CCHHHHHHHHHHHHHCC-CCCCCC---CCEECCCCCCCCEEEECCHHHHHCCCCHHHHHHHHHHCCCCCCCEEEEEEECCEEEEEECHHHHHHHHHCC----CC---
PSA

>P1;d1f7ua3
8926831760393710797408715063513000100003102710a2722700400480879a50301010450737-c3736610760086043860064041753400010368025722653478379748

>P1;d1iq0a3
----------------------------51464006200500580-927451---607706ab550410030590197386736600540365073281045031480500040487046726858----9a---


Translating the sequences
****************************CHHHHHHHHHHHHHHHH*CCCHHH***HCEECCCHHHCCEEEEHHHH***-CCCHHHHHHHHHHCCCCCCCEEEEEEECCEEEEEECHHHHHHHHHHH****HH***
----------------------------C*HHHHHHHHHHHHH**-CCC***---*CEECCC***CCEEEE**HHHHH*CCCHHHHHHHHHHCCCCCCCEEEEEEECCEEEEEECHHHHHHHHH**----**---

55190.tem
_________________________________
----------------------------CHHHHHHHHHHHHHHHH-CCCHHH---HCEECCCHHHCCEEEEHHHHHHH-CCCHHHHHHHHHHCCCCCCCEEEEEEECCEEEEEECHHHHHHHHHHH----HH---




Structural block scores
0	27	-	3.0	P	  4.6  75.0

29	44	H	4.6	H	  1.2  2.6

46	48	C	5.0	H	  6.5  6.0

49	51	H	3.0	P	  3.7  3.3

52	54	-	3.0	P	  1.3  75.0

57	58	E	5.0	H	  6.0  7.0

59	61	C	5.0	H	  5.0  5.5

62	64	H	3.0	P	  8.2  7.2

65	66	C	5.0	H	  1.5  2.0

67	70	E	5.0	H	  0.5  1.0

71	77	H	3.6	M	  3.7  4.4

79	81	C	5.0	H	  7.5  7.0

82	91	H	5.0	H	  3.7  3.3

92	98	C	5.0	H	  3.9  3.7

99	105	E	5.0	H	  3.1  2.4

106	107	C	5.0	H	  4.0  4.0

108	113	E	5.0	H	  0.8  1.5

115	125	H	4.6	H	  4.2  5.5

126	129	-	3.0	P	  5.5  75.0

130	131	H	3.0	P	  8.0  9.8

132	134	-	3.0	P	  6.3  75.0

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