Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d6t0bf-
CCCCHHHHHHHHHHHHC--CCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHCHHHHHHHCCCCHHHHC-CC

>P1;d7cohe-
---CHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCC
PSA

>P1;d6t0bf-
6b254860173037305--708548105401940074b22024600430040064172660017001305930-86784067118705801761702045647-7b

>P1;d7cohe-
---7a9821770284054790-6663065008402a4b41051500300030063284593008004305820886983166006304700861a03004533548


Translating the sequences
***CHHHHHHHHHHHH*--CC*CHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHC-CCCHHHHHHHHH*HHHHHHHCCCCHHHHC-CC
---CHHHHHHHHHHHHH**CC-CHHHHHHHHHHH*CCCCCCCHHHHHHHHHHHHH*CCHHHHHHHHHHHHHHC*CCC*HHHHHHHHHHHHHHHHCCCC****C*CC

48479.tem
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---CHHHHHHHHHHHHH--CC-CHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHCCCCHHHHC-CC




Structural block scores
0	2	-	3.0	P	  6.5  75.0

4	16	H	4.8	H	  3.6  4.9

17	18	-	3.0	P	  75.0  5.5

19	20	C	5.0	H	  3.5  4.5

23	34	H	4.8	H	  3.0  3.3

35	41	C	5.0	H	  4.1  5.1

42	55	H	4.9	H	  2.3  1.6

56	57	C	5.0	H	  4.5  6.0

58	71	H	5.0	H	  2.9  3.4

74	76	C	5.0	H	  7.0  7.7

77	93	H	4.8	H	  4.1  3.5

94	97	C	5.0	H	  2.2  3.4

98	101	H	3.0	P	  4.8  3.0

104	105	C	5.0	H	  9.2  6.0

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