Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1qh4a1
CCCCHHHHHHHHCCHHHHCCCCCCCCCHHHHHCCHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHCHHHHHHHHHHHCCCCCC

>P1;d4am1a1
--CCHHHHHHHHHHHHHHH-HCCCCCCHHHHHCCHHHHHHHCCCCCCCCCCCHHHHHHHHHCCC----CCCCCCCCCCHHHHHCHHHHHHHHHHHCCCCCC
PSA

>P1;d1qh4a1
aa638707512866275221908803000061065710660063508742002400640267338699263106123a506820550034033556b6875

>P1;d4am1a1
--08a72386046107406-828a090102620667104502544098410024005400763a----2b3007112a5059303300730353669a88a


Translating the sequences
**CCHHHHHHHH**HHHH***CCCCCCHHHHHCCHHHHHHHCCCCCCCCCCHHHHHHHHHHCCC****CCCCCCCCCC*HHHHCHHHHHHHHHHHCCCCCC
--CCHHHHHHHHHHHHHHH-HCCCCCCHHHHHCCHHHHHHHCCCCCCCCCC*HHHHHHHHHCCC----CCCCCCCCCCHHHHHCHHHHHHHHHHHCCCCCC

48034.tem
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--CCHHHHHHHHHHHHHHH-HCCCCCCHHHHHCCHHHHHHHCCCCCCCCCCHHHHHHHHHHCCC----CCCCCCCCCCHHHHHCHHHHHHHHHHHCCCCCC




Structural block scores
0	1	-	3.0	P	  10.5  75.0

2	3	C	5.0	H	  4.5  4.0

4	18	H	4.6	H	  4.5  4.3

21	26	C	5.0	H	  3.2  4.9

27	31	H	5.0	H	  1.4  2.2

32	33	C	5.0	H	  3.0  3.0

34	40	H	5.0	H	  3.6  3.3

41	50	C	5.0	H	  3.5  3.7

51	60	H	4.8	H	  2.4  2.2

61	63	C	5.0	H	  4.3  6.5

64	67	-	3.0	P	  8.0  75.0

68	77	C	5.0	H	  3.5  3.8

78	82	H	4.6	H	  4.2  4.4

84	94	H	5.0	H	  3.0  3.0

95	100	C	5.0	H	  7.2  8.7

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