Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1n62a2
--CEEEEEEECCEEEEE-EECCCCCHHHHHHHCCCCCCCCCCCC------CCCCCCCEEEEC----------CEEEEHHHCCHHHHCCCEEECHHHCC-

>P1;d3hrdd1
CCCEEEEEEECCEEEEE-EECCCCCHHHHHHCCCCCCCCCCCCC------CCCCCCCEEEEC----------CEEEEHHHCCHHHHCCEEEECHHHCCC

>P1;d3iam31
----CEEEECCCCEEEE---CCCCCHHHHHH-HHCCC-CCCCCCCCCCCCCCCCCCCEEEEECCC----CCCCCCEECCCCCC--CCCCEEEC------

>P1;d3nvva1
-CCCCEEEEECCEEEEECCCCCCCCHHHHHHHCCCCCCCCCCCC------CCCCCCCEEEEEEEECCCCEEEEEEEECCCCCHHHCCCCEEECHHHCC-
PSA

>P1;d1n62a2
--545060301988162-6056923004002642825516362a------638324040505----------9671301515026059060307427b-

>P1;d3hrdd1
5b545070401978452-60428230030038307172063625------717454030525----------87632005170370390504074269a

>P1;d3iam31
----6170402854161---66b12017004-60627-05373169a795706253020400327----a2589530004370--56802041------

>P1;d3nvva1
-c7a5020402a95131691679340020027623364066434------8193540404014519a677625463300514036057140207317b-


Translating the sequences
--C**EEEEECCEEEEE-**CCCCCHHHHHH*CCCCCCCCCCCC------CCCCCCCEEEE*----------CEEEE***CCHHH*CCCEEECHHHCC-
**C**EEEEECCEEEEE-**CCCCCHHHHHH*CCCCCCCCCCCC------CCCCCCCEEEE*----------CEEEE***CCHHH*CC*EEECHHHCC*
----*EEEE*CC*EEEE---CCCCCHHHHHH-**CCC-CCCCCC******CCCCCCCEEEE****----***C**EE***CC*--*CCCEEEC------
-*C**EEEEECCEEEEE***CCCCCHHHHHH*CCCCCCCCCCCC------CCCCCCCEEEE************EEEE***CCHHH*CCCEEECHHHCC-

54292-2.tem
_________________________________
-*C**EEEEECCEEEEE-**CCCCCHHHHHH*CCCCCCCCCCCC------CCCCCCCEEEE****----***CEEEE***CCHHH*CCCEEECHHHCC-




Structural block scores
3	4	*	1.6	P	  4.5  4.5  40.5  7.8

5	9	E	4.9	H	  1.8  2.2  2.4  1.2

10	11	C	5.0	H	  5.0  5.0  5.0  6.2

12	16	E	4.9	H	  5.0  5.2  3.4  3.8

18	19	*	2.3	P	  3.0  3.0  75.0  5.0

20	24	C	5.0	H	  5.0  3.8  5.3  5.8

25	30	H	5.0	H	  1.0  1.0  2.0  0.7

32	43	C	4.8	H	  4.5  3.5  9.6  3.9

44	49	-	4.3	M	  75.0  75.0  7.8  75.0

50	56	C	5.0	H	  3.7  4.0  3.3  4.3

57	60	E	5.0	H	  2.2  2.5  1.5  2.0

61	64	*	2.9	P	  57.5  57.5  3.0  2.8

65	68	-	4.3	M	  75.0  75.0  75.0  8.1

69	71	*	3.5	M	  75.0  75.0  5.8  5.0

73	76	E	4.7	H	  4.2  4.5  4.2  4.0

77	79	*	1.0	P	  2.0  1.7  1.3  1.7

80	81	C	5.0	H	  3.0  4.0  5.0  2.5

82	84	H	4.3	M	  2.7  3.3  50.0  3.0

86	88	C	4.8	H	  4.7  4.0  4.7  4.3

89	91	E	5.0	H	  3.0  3.0  2.0  2.0

93	95	H	4.3	M	  4.3  4.3  75.0  3.7

96	97	C	4.3	M	  9.2  7.5  75.0  9.2

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