Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1lr0a1
CCCCHHHHCCHHHHHHHHHHHHH---HHHHHHHHHHHHHCCCCCCCCCCCEEEEEEC-CCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCEEEEEC-HHHHHC---

>P1;d1u07a-
------------------CCCCCEEECCCCCCCHHHHH------HCCCEEEEEEEEECCCCCEEEEEEEEEECCCCCHHHHHHHHCCC-EECC--------CCCEEEEEEEEEECCCCCCCCC

>P1;d3qdpa-
------------CCCHHHHHHHC---CCCCCC-CCHHHHCC-------CCEEEEEEECCCCCEEEEEEEEE--CHHHHHHHHHHHCCC-CCCCCCC--HHHHHHC-EEEEEEC-C--------
PSA

>P1;d1lr0a1
c9a77898577995887779439---7137303720174086194178a50201035-16240450522850a4950061027004608612458176941474146250504-035049---

>P1;d1u07a-
------------------ba71716555a1711a7068------583524040402036904077141450656a1026203300540-4036--------9645742325150639b9a7aa

>P1;d3qdpa-
------------c7649603b40---810480-a608726b-------53020304026707144064487--185008201700690-a048025--9903640-6041406-1--------


Translating the sequences
***************HHHHHHH*---*******HHHHHHCC****CCCCCEEEEEE*-CCCC**EEEEEE**CCHHHHHHHHHHH****CCCCCCC**HHHHHHC**EEEEEC-*****C---
------------------****C***CCCCCC*HHHHH------*CCC**EEEEEEECCCCCEEEEEEEEE*CC***HHHHHHHHCCC-**CC--------*****EEEEEE**C****C***
------------***HHHHHHHC---CCCCCC-**HHHHCC-------CCEEEEEEECCCCCEEEEEEEEE--CHHHHHHHHHHHCCC-CCCCCCC--HHHHHHC-EEEEEEC-C--------

74653.tem
_________________________________
------------***HHHHHHHC---CCCCCC*HHHHHHCC---*CCCCCEEEEEEECCCCCEEEEEEEEE*CCHHHHHHHHHHHCCC-CCCCCCC--HHHHHHC*EEEEEEC-C****C---




Structural block scores
0	11	-	4.0	M	  8.2  75.0  75.0

12	14	*	2.7	P	  7.3  75.0  8.5

15	21	H	4.0	M	  6.4  36.4  5.4

23	25	-	4.0	M	  75.0  4.0  75.0

26	31	C	4.0	M	  3.5  4.9  3.5

33	38	H	4.5	M	  3.5  17.8  5.6

39	40	C	4.0	M	  4.0  75.0  8.8

41	43	-	4.0	M	  5.3  75.0  75.0

45	49	C	4.0	M	  6.3  4.4  46.6

50	56	E	4.9	H	  1.6  1.4  1.3

57	61	C	4.8	H	  17.6  4.4  4.4

62	70	E	4.7	H	  3.4  3.2  4.2

72	73	C	4.5	M	  7.2  5.5  38.0

74	84	H	4.7	H	  2.7  2.5  2.8

85	87	C	4.0	M	  3.3  3.0  5.0

89	95	C	4.3	M	  3.9  34.0  4.2

96	97	-	4.0	M	  6.5  75.0  75.0

98	103	H	4.0	M	  4.8  40.7  5.2

106	111	E	4.8	H	  3.0  2.8  2.5

115	118	*	2.7	P	  3.0  8.1  75.0

120	122	-	4.0	M	  75.0  9.3  75.0

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