Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d3db7a1
CCCCCCCCCCC-CHHHHHHHHHHCC-CCEEEEECCCCC-CCEEEEECCCCEEEEC--CCEEEEECCCCCCCHHHCCHHHHHHHHH-HCCCCCEEEEEEC-CCEEEEECC-CEEEECCCCCEEEEEC

>P1;d4dsda-
--CCEEECCCCCCHHHHHHHHHHCCCCCCCEEEEEECCCEEEEEECC-CCEEEECCCCCEEEEECCCCCCCHHHCCHHHHHHHHHCCCCCCCEEEEEEECCEEEEEECCCCEEEEC-CCCCCCC--
PSA

>P1;d3db7a1
9b634628386-3760161187108-3424501256aa-6141030555020104--0614101055620378002a50383056-425a050220337-931404036-040304493724436a

>P1;d4dsda-
--a655275850265047118710a9292550322569622130207-403020338061320306e6402a6002a205920875a36a35022033787022030366530605-7184398--


Translating the sequences
**CC***CCCC-CHHHHHHHHHHCC-CCEEEEE***CC-**EEEEEC*CCEEEEC--CCEEEEECCCCCCCHHHCCHHHHHHHHH-HCCCCCEEEEEE*-C*EEEEECC-CEEEEC*CCCEEEE**
--CCEEECCCC*CHHHHHHHHHHCC*CC**EEEEEECC*EEEEEE*C-CCEEEEC**CCEEEEECCCCCCCHHHCCHHHHHHHHH**CCCCCEEEEEEE*CEEEEEECC*CEEEEC-CCC****--

160574.tem
_________________________________
--CCEEECCCC-CHHHHHHHHHHCC-CCEEEEEEEECC-EEEEEEEC-CCEEEEC--CCEEEEECCCCCCCHHHCCHHHHHHHHH-HCCCCCEEEEEEE-CEEEEEECC-CEEEEC-CCCEEEE--




Structural block scores
0	1	-	3.0	P	  10.2  75.0

2	3	C	5.0	H	  4.5  8.2

4	6	E	3.0	P	  4.0  4.0

7	10	C	5.0	H	  6.2  6.2

13	22	H	5.0	H	  3.8  4.0

23	24	C	5.0	H	  4.0  5.2

26	27	C	5.0	H	  3.5  5.5

28	35	E	3.8	M	  3.1  3.0

36	37	C	5.0	H	  10.5  7.5

39	45	E	4.1	M	  2.1  1.4

48	49	C	5.0	H	  2.5  2.0

50	53	E	5.0	H	  0.8  1.2

55	56	-	3.0	P	  75.0  5.5

57	58	C	5.0	H	  3.0  3.0

59	63	E	5.0	H	  1.4  1.8

64	70	C	5.0	H	  3.0  4.6

71	73	H	5.0	H	  5.0  5.5

74	75	C	5.0	H	  1.0  1.0

76	84	H	5.0	H	  4.5  4.8

87	91	C	5.0	H	  4.5  5.5

92	98	E	4.7	H	  2.4  2.4

101	106	E	4.7	H	  2.0  1.2

107	108	C	5.0	H	  4.5  4.5

111	114	E	5.0	H	  1.8  2.2

117	119	C	5.0	H	  6.3  5.3

120	123	E	3.0	P	  3.2  6.0

124	125	-	3.0	P	  8.2  75.0

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