Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1b4ra-
----------------------CEEECCCC---CCCCCEEEEEEEECCC---CCCEEEEECCCCCCEEEEECC----EEEEEECCCEEEEEEEEEECCCCEEEEEEEEEECC-------

>P1;d1l0qa1
---------------CCCCCCC--EEECCCC-CEEECCCCEEEEECCC----CCCEEEEECCCC---CEECCC----CCEECCCCCEEEEEEEEEEECCEEEEEEEEEEEECCCCCCCC

>P1;d1wgoa1
CCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEEEECCCCCCCCCEEEEECCCCCEEEEECHHHHCCCEEEECCCCCCEEEEEEEECCCCEEEEEEEECC---------
PSA

>P1;d1b4ra-
----------------------06440528---906236506040451a---708605020809568181933----61304088347160305071ba8509031608096-------

>P1;d1l0qa1
---------------7860505--0615095-9203374504040508----60762505032b---542784----505140a8387150403021a455433444020268c3952f

>P1;d1wgoa1
caa9a8a998aaa9b685650860906179b2a53837740304080760954506060405484744342018588306170a85851704080809047151615050---------


Translating the sequences
----------------------C*EE*CCC---CCCCC*EEEEEEECCC---CCCEEEEECCCCC*EEEE*CC----*EEEE*CCCEEEEEEEEEECCCCEEEEEEEEEE*C-------
---------------CCCCCCC--EEECCCC-C***CCC*EEEEE*CC----CCCEEEEECCCC---*EECCC----C*EE*CCCCEEEEEEEEEE*CC*EEEEEEEEEE*C*******
***************CCCCCCCC*EEE*CCC*CCCCCCCEEEEEEECCC***CCCEEEEECCCCC*EEEEC******CEEEECCCC**EEEEEEEECCCCEEEEEEEE**---------

49299.tem
_________________________________
---------------CCCCCCCC*EEECCCC-CCCCCCCEEEEEEECCC---CCCEEEEECCCCC*EEEECCC----CEEEECCCCEEEEEEEEEECCCCEEEEEEEEEE*C-------




Structural block scores
0	14	-	4.0	M	  75.0  75.0  10.0

15	22	C	4.0	M	  65.6  13.2  5.5

24	26	E	4.7	H	  2.7  2.3  5.0

27	30	C	4.5	M	  22.5  4.8  7.1

32	38	C	4.3	M	  14.4  4.0  6.2

39	45	E	4.7	H	  2.7  2.6  2.7

46	48	C	4.7	H	  5.5  27.7  4.3

49	51	-	4.0	M	  75.0  75.0  4.7

52	54	C	5.0	H	  5.0  4.3  3.0

55	59	E	5.0	H	  2.6  3.6  3.2

60	64	C	4.8	H	  4.4  18.3  4.2

66	69	E	4.5	M	  4.5  21.5  3.8

70	72	C	4.0	M	  5.0  6.3  1.0

73	76	-	4.0	M	  75.0  75.0  7.2

78	81	E	4.5	M	  2.0  2.5  3.5

82	85	C	4.8	H	  4.8  5.4  5.9

86	95	E	4.8	H	  3.3  3.0  4.1

96	99	C	4.5	M	  7.8  5.1  3.2

100	109	E	4.8	H	  3.2  2.9  3.1

112	118	-	4.0	M	  75.0  8.9  75.0

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