Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1r8ha-
C-------------------------------CEEEEEEEEE-CHHHHHHHHHHHHHHCHHHCCCCCCCCCCCCC-----------CCCCCCEEEEEECCCHHHHHHHHHHCCCCC--------CCEEEEEEEE---HHHC

>P1;d2bopa-
----------------------------------CEEEEEEE-CHHHHHHHHHHHHHHCHHHCCEECCCEEEECCC---------CCCEEEEEEEEEEECCHHHHHHHHHHCCCCC--------CCEEEEEECC---CC-C

>P1;d6vh6a1
CCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEECCHHHHHHHHHHHHHHCCCC--EECCCEEEECCCCCCCCCCCHHHCEEEEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCHHHEEEEEEEEEEEE-CCC
PSA

>P1;d1r8ha-
9-------------------------------a500102001-73830480276037626920361481375879-----------a162a510010006569117601740a139--------6083737435---5a64

>P1;d2bopa-
----------------------------------70202010-859305402850665157205705914377288---------c8546b6020304065683264047508329--------b082535759---88-b

>P1;d6vh6a1
9c8a8557145006404820873928253b74613000202205780041024004500640--5137164253ba92593957387250a512020001155004101500550077285413806062252aa04-b2a


Translating the sequences
C-------------------------------CEEEEEEEEE-CHHHHHHHHHHHHHHCHHHCC**CCC****CC-----------CC****EEEEEE*CCHHHHHHHHHHCCCCC--------CCEEEEEEEE---***C
----------------------------------*EEEEEEE-CHHHHHHHHHHHHHHCHHHCCEECCCEEEECCC---------*CCEEEEEEEEEEECCHHHHHHHHHHCCCCC--------CCEEEEEE**---*C-C
C*******************************CEEEEEEEEE*CHHHHHHHHHHHHHHC***--EECCCEEEECCC***********CEEEEEEEEEEECCHHHHHHHHHH***************EEEEEEEE***-C*C

54957.tem
_________________________________
C-------------------------------CEEEEEEEEE-CHHHHHHHHHHHHHHCHHHCCEECCCEEEECCC---------*CCEEEEEEEEEEECCHHHHHHHHHHCCCCC--------CCEEEEEEEE---*C*C




Structural block scores
1	31	-	4.0	M	  75.0  75.0  5.1

33	41	E	4.8	H	  1.0  9.7  1.1

44	57	H	5.0	H	  4.1  4.1  2.5

59	61	H	4.0	M	  5.7  4.7  3.3

62	63	C	4.0	M	  1.5  2.5  75.0

64	65	E	4.0	M	  3.5  3.5  3.0

66	68	C	5.0	H	  4.3  5.0  3.7

69	72	E	4.0	M	  5.8  5.2  4.2

73	75	C	4.7	H	  30.3  6.0  8.3

76	84	-	4.0	M	  75.0  75.0  5.8

86	87	C	4.5	M	  5.8  6.5  4.5

88	98	E	4.5	M	  2.3  3.3  2.3

99	100	C	5.0	H	  5.5  5.5  1.0

101	110	H	5.0	H	  4.2  4.5  2.1

111	115	C	4.0	M	  4.7  4.4  2.0

116	123	-	4.0	M	  75.0  75.0  4.6

124	125	C	4.0	M	  3.0  5.8  4.0

126	133	E	4.8	H	  5.0  5.5  4.2

134	136	-	4.0	M	  75.0  75.0  4.8

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