Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1dt9a3
CCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCC-CCCCCCEEEEEEEEECHHHCEEEEEEEEC-CCCCCCCCEEEEECCCCCHHHHHHCCC

>P1;d4af1a1
CC--CHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCEEEEEEEEECCCCCCCCCEEEEECCCCCCCCCCCCCC
PSA

>P1;d1dt9a3
c689856642650662188058260986000000001927184057206644880493777a6283126005302620662c-4018200000002153a776777243123-024069331252344020710571185

>P1;d4af1a1
46--649714850541196039470475000000003934076037405723760673a7872361026006303730761a64037200000000046abb8472115004000450981512245401063038208a


Translating the sequences
CC**CHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHH**CCC*HHHHHHHHHHHHHHHHH**CC-CCCCCCEEEEEEEEECHHHCEEEEEEEE*-CCCCCCCCEEEEECCCCCHHHHHHCCC
CC--CHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC*CCCCCCEEEEEEEEEC***CEEEEEEEEE*CCCCCCCCEEEEECCCCC******CCC

55481.tem
_________________________________
CC--CHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC-CCCCCCEEEEEEEEECHHHCEEEEEEEEE-CCCCCCCCEEEEECCCCCHHHHHHCCC




Structural block scores
0	1	C	5.0	H	  9.2  5.0

2	3	-	3.0	P	  8.5  75.0

5	20	H	5.0	H	  4.4  4.2

21	28	C	5.0	H	  4.9  4.5

29	34	E	5.0	H	  0.0  0.0

35	39	C	5.0	H	  3.8  3.8

40	56	H	4.8	H	  4.5  4.1

57	59	C	5.0	H	  5.7  6.8

60	79	H	4.7	H	  3.8  3.5

80	81	C	5.0	H	  7.2  5.8

83	88	C	5.0	H	  2.5  2.7

89	97	E	5.0	H	  0.9  0.4

99	101	H	3.0	P	  8.2  11.2

103	111	E	4.8	H	  4.0  2.7

113	120	C	5.0	H	  3.4  3.4

121	125	E	5.0	H	  2.6  2.8

126	130	C	5.0	H	  2.0  2.0

131	136	H	3.0	P	  3.5  3.7

137	139	C	5.0	H	  4.7  6.2

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