Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1mbya-
---------------------------------CCCEEEEEEEECCCEEEEEEEECCCCEEEE------EEEC----CEEEEECCCCCEEEEECC----CCCCHHHHHHHCC------------CCCEEEEECC

>P1;d3rq7a1
CHHHHHHHHHHHHHCCCCCCCCCCHHHHCCHHHCCCCCEEEEEECCCCCEEEEEECCCCEEEEEC-CCCEEEECCCCCEEEEECCCCCEEEEECC-----CCCHHHHHHHHHHHHHHHHHHHCCCCCCCCC---

>P1;d3rq7a2
---------------------------------CCC--EEEEEECC--CEEEEEECCCCEEEEECCCCCEEEEECCCCEEEEECCCCCEEEEEHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC----------
PSA

>P1;d1mbya-
---------------------------------b77551304548345243212236875665------8844----84262628888456126b----5913760385178------------816636757b

>P1;d3rq7a1
aa966798568688565877b756a8887679765553500624558630402020480000506-46140104762440201468774561417-----815b90572051047038506755b279655---

>P1;d3rq7a2
---------------------------------a27--4545262a--5020223174002030472802031258760001125885665353650967826850351273074045506877----------


Translating the sequences
---------------------------------CCC**EEEEEECCC**EEEEEECCCCEEEE------EEE*----CEEEEECCCCCEEEEECC----*CCCHHHHHHH**------------CCC*******
*********************************CCC**EEEEEECCC*CEEEEEECCCCEEEEEC-CCCEEEE*CCCCEEEEECCCCCEEEEECC-----CCCHHHHHHHHHHHHHHHHHHHCCCCC****---
---------------------------------CCC--EEEEEECC--CEEEEEECCCCEEEEEC*CCCEEEE*CCCCEEEEECCCCCEEEEE*******CCCHHHHHHHHHHHHHHHHHHHCC----------

82615.tem
_________________________________
---------------------------------CCC**EEEEEECCC*CEEEEEECCCCEEEEEC-CCCEEEE*CCCCEEEEECCCCCEEEEECC----*CCCHHHHHHHHHHHHHHHHHHHCCCCC****---




Structural block scores
0	32	-	4.0	M	  75.0  7.4  75.0

33	35	C	5.0	H	  8.5  5.3  6.5

36	37	*	2.7	P	  5.0  4.0  75.0

38	43	E	5.0	H	  2.8  2.8  4.3

44	46	C	4.7	H	  5.0  6.0  29.2

49	54	E	5.0	H	  2.3  1.3  1.5

55	58	C	5.0	H	  6.0  3.0  3.0

59	63	E	4.8	H	  19.4  1.0  1.0

66	68	C	4.0	M	  75.0  3.7  3.3

69	72	E	4.8	H	  6.0  1.2  1.5

74	77	C	4.2	M	  58.2  4.8  6.5

78	82	E	5.0	H	  4.0  1.4  0.4

83	87	C	5.0	H	  6.8  6.4  5.6

88	92	E	5.0	H	  3.6  4.0  5.0

93	94	C	4.0	M	  8.8  4.0  4.5

95	98	-	4.0	M	  75.0  75.0  5.0

100	102	C	5.0	H	  4.3  4.7  5.3

103	121	H	4.4	M	  41.8  4.2  3.8

122	126	C	4.0	M	  33.0  6.1  47.8

127	130	*	2.7	P	  5.5  6.2  75.0

131	133	-	4.0	M	  7.8  75.0  75.0

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