Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1i17a-
------CCCCCCCCEEECCCCCCCCCCC-HHHHHHHHHHHHHCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHC------------CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCC

>P1;d1u3ma1
CCCCCC------CCEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCEECCCC-CCCCHHHHHHHHHHHHHHHCC-CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---

>P1;d4hlsa-
-----C------CCEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEECCHH-HCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC-----------HHHHHHHHHHHHHHHHHHHHHHC------
PSA

>P1;d1i17a-
------594a6250005456553b0808-98059106633730002041813785c12586018601610540197407845a------------a364007002400541037270b418b5aaf

>P1;d1u3ma1
dca7ba------834518814b1b1a397891761551145250330235a29-883629520410160015435-00933988b5b974889595353236004400420041225676a6b---

>P1;d4hlsa-
-----e------94531a52a12a090b6a62171068239400330205429-61b63a501720161018424650675a6906-----------92046005400430024016646------


Translating the sequences
------******CCEE*CCCCCCCCCCC-HHHHHHHHHHHHHCCC**E*CCCC*CCCCHHHHHHHHHHHHHHHCHHHHH***C------------**HHHHHHHHHHHHHHHHH*****C*CC***
*****C------CCEECCCCCCCCCCCCCHHHHHHHHHHH**CCCCCEECCCC-CCCCHHHHHHHHHHHHHHHC*-***CCCCCCC***********HHHHHHHHHHHHHHHHHHHHHH**CC---
-----C------CCEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEECC**-*CCCHHHHHHHHHHHHHHH*HHHHHCCCCCCC-----------HHHHHHHHHHHHHHHHHHHHHHC------

54098.tem
_________________________________
-----C------CCEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEECCCC-CCCCHHHHHHHHHHHHHHHCHHHHHCCCCCCC---------**HHHHHHHHHHHHHHHHHHHHHHC*CC---




Structural block scores
0	4	-	4.0	M	  75.0  11.0  75.0

6	11	-	4.0	M	  6.1  75.0  75.0

12	13	C	5.0	H	  2.5  5.5  6.5

14	15	E	5.0	H	  0.0  4.5  4.0

16	28	C	4.8	H	  10.4  5.9  5.3

29	41	H	4.8	H	  4.6  4.2  4.6

42	46	C	4.6	H	  0.4  2.2  1.2

47	48	E	4.5	M	  2.5  2.5  1.0

49	52	C	4.5	M	  4.8  6.6  5.0

54	57	C	4.8	H	  5.1  6.2  6.1

58	72	H	5.0	H	  3.4  2.7  3.3

74	78	H	4.0	M	  5.4  17.8  4.2

79	85	C	4.1	M	  36.1  6.8  6.2

86	94	-	4.0	M	  75.0  7.8  75.0

95	96	*	2.7	P	  6.8  4.0  75.0

97	118	H	4.8	H	  3.1  2.7  2.7

121	122	C	4.0	M	  8.2  8.8  75.0

123	125	-	4.0	M	  14.5  75.0  75.0

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