Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1j6ua1
--------CEEEECCCCCCCHHHHHHHHCCCCEEEECCC-CCHHHHHHHHCCCCEEC-CCCCCCCC--CCCEEEECCCCCCCCHHHHHHC-CCCCEEC

>P1;d1p3da1
CCCCCCCCEEEEECCCCCCCHHHHHHHHHCCEEEEEECC-CCHHHHHHHHCCCEEEE-CCCHHHHC--CCCEEEECCCCCCCCHHHHHHHHCCCCEEC

>P1;d2wjpa1
--CCCCCCCEEEECCHHHHHHHHHHHHCCCCCCEEEECCCCCCCHHHCCC-CCCEEECCCCHHHHH--CCCEEEECCCCCCCCHHHHHHHHCCCEEEC

>P1;d3eaga1
-------CEEEEECCCCCCCHHHHHHHHCCCEEEEEECC-CCC-CHHHHHCCCEEEE-CCCHHHHHCCCCCEEEECCCCCCC-CHHHHHHHCCCCEEC
PSA

>P1;d1j6ua1
--------30000200a9c0760272376a470000077-53820740393905031-61449005--8083021599078714007405-5916078

>P1;d1p3da1
aa868838200002018ac19603721768170000188-48a50660495807043-71368109--602101149808a81400600675916169

>P1;d2wjpa1
--6826c450000203a701720750384a050200045780612a804a-90733106026a104--505000038a18793810560584a17145

>P1;d3eaga1
-------821000007bba2840481395a460000276-768-6681884908336-636360096460520126c60979-601320386a15579


Translating the sequences
--------*EEEECCCCCCCHHHHHHHHCCC*EEEE*CC-CC**HHHHHHCCC*EE*-CCC*****--CCCEEEECCCCCCCCHHHHHH*-CCCCEEC
*******C*EEEECCCCCCCHHHHHHHH*CC*EEEEECC-CC**HHHHHHCCC*EEE-CCCHHHH*--CCCEEEECCCCCCCCHHHHHHHHCCCCEEC
--*****C*EEEECC*****HHHHHHH*CCC**EEEECC*CC**HHH***-CC*EEE*CCCHHHH*--CCCEEEECCCCCCCCHHHHHHHHCCC*EEC
-------C*EEEECCCCCCCHHHHHHHHCCC*EEEEECC-CC*-*HHHHHCCC*EEE-CCCHHHH***CCCEEEECCCCCCC-*HHHHHHHCCCCEEC

51984.tem
_________________________________
--*****C*EEEECCCCCCCHHHHHHHHCCC*EEEEECC-CC**HHHHHHCCC*EEE-CCCHHHH*--CCCEEEECCCCCCCCHHHHHHHHCCCCEEC




Structural block scores
0	1	-	4.3	M	  75.0  10.5  75.0  75.0

2	6	*	3.5	M	  75.0  6.6  6.9  75.0

9	12	E	5.0	H	  0.0  0.0  0.0  0.2

13	19	C	4.5	M	  4.9  5.0  3.4  6.1

20	27	H	4.9	H	  4.2  4.4  4.0  4.6

28	30	C	4.8	H	  6.8  5.0  4.8  6.5

32	36	E	4.7	H	  0.0  0.2  0.4  0.4

37	38	C	5.0	H	  7.0  8.0  4.5  6.5

40	41	C	5.0	H	  4.0  6.0  4.0  6.5

42	43	*	1.6	P	  5.0  7.8  3.5  41.5

44	49	H	4.5	M	  3.8  4.2  5.8  6.2

50	52	C	4.8	H	  4.0  4.3  28.0  4.3

54	56	E	4.8	H	  1.3  2.3  2.3  4.0

58	60	C	5.0	H	  3.7  3.7  2.7  5.0

61	64	H	4.3	M	  3.2  3.8  4.4  2.2

66	67	-	4.3	M	  75.0  75.0  75.0  5.0

68	70	C	5.0	H	  5.3  2.7  3.3  3.7

71	74	E	5.0	H	  1.5  0.8  0.0  1.2

75	82	C	4.9	H	  5.8  6.1  6.2  15.6

83	90	H	4.7	H	  11.9  2.9  4.1  2.9

91	94	C	4.8	H	  5.2  5.2  5.6  5.6

95	96	E	5.0	H	  3.5  3.5  2.5  6.0

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