Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1uz5a1
-CCEEEE-CC-CCCC---CCEEEEEEECC------CCEEECCC-CCCHHHHHHHCCEEEEECCC-------CCCCCEEEEECCC---C

>P1;d1wu2a1
-CCEEEEEECCCEECCCCCCEEEEEEEEC------CEEEECCCCCCCCCHHHHHCCEEEEECC---CCCEECCCCEEEEEEC------

>P1;d2nqra1
CCCCEEEEECCCCCCCCCCCEEEEEEEEECCC-CCEEEEECCCCCCCCCCHHHHCCEEEEECC---CCCCCCCCCEEEEEECCHHHCC

>P1;d6fgca3
-CCEEEEEECCCEECCC-CCEEEEEEEECCCCCCCCEEEECC------CHHHCCCCEEEEECCCCCCCCEECCCCEEEEEECCCC---
PSA

>P1;d1uz5a1
-8a5450-04-72b2---9444140304a------94010179-a48a9528731403133569-------a787815013598---b

>P1;d1wu2a1
-775250505350807596525220326a------64040175868c3660576040203045---9280277845060035------

>P1;d2nqra1
959355050315080959954401030573b8-563204307825a75860286040200057---9245066445030230998396

>P1;d6fgca3
-7732504017527036-8444560003449b484010543d------a3963a10030204437ba7521661540302236a4---


Translating the sequences
-CCEEEE-*C-C**C---CCEEEEEEE*C------C*EEECCC-CCC**HHHHHCCEEEEECC*-------CCCC*EEEEECC*---*
-CCEEEEEECCC**CCC*CCEEEEEEEEC------CEEEECCC*CCC*CHHHHHCCEEEEECC---CCC**CCCCEEEEEEC------
*CC*EEEEECCC**CCC*CCEEEEEEEE****-***EEEECCC*CCC*C*HHHHCCEEEEECC---CCC**CCCCEEEEEECC*****
-CCEEEEEECCC**CCC-CCEEEEEEEEC******CEEEECC------CHHH**CCEEEEECC***CCC**CCCCEEEEEECC**---

63867.tem
_________________________________
-CCEEEEEECCC**CCC*CCEEEEEEEEC***-**CEEEECCC*CCC*CHHHHHCCEEEEECC*--CCC**CCCCEEEEEECC**--*




Structural block scores
1	2	C	5.0	H	  9.2  7.0  7.0  7.0

3	8	E	4.7	H	  14.8  2.8  3.0  2.3

9	11	C	4.8	H	  28.7  4.3  3.0  4.3

12	13	*	1.0	P	  6.8  4.0  4.0  4.5

14	16	C	4.5	M	  50.7  4.0  4.7  3.0

18	19	C	5.0	H	  6.5  5.5  7.0  6.0

20	27	E	4.9	H	  2.5  2.8  2.1  2.8

29	31	*	3.5	M	  75.0  75.0  7.5  8.2

33	34	*	3.5	M	  75.0  75.0  5.5  6.0

36	39	E	4.8	H	  1.2  2.0  2.2  2.5

40	42	C	4.8	H	  5.7  4.3  5.0  30.5

44	46	C	4.3	M	  7.5  8.8  7.5  75.0

49	53	H	4.6	H	  5.0  4.8  4.4  6.3

54	55	C	5.0	H	  2.5  2.0  2.0  0.5

56	60	E	5.0	H	  2.0  1.0  0.4  1.0

61	62	C	5.0	H	  5.5  4.5  6.0  4.0

64	65	-	4.3	M	  75.0  75.0  75.0  9.2

66	68	C	4.3	M	  75.0  6.3  5.0  7.5

69	70	*	2.3	P	  75.0  1.0  2.5  1.5

71	74	C	5.0	H	  8.1  6.5  5.0  4.5

75	80	E	4.9	H	  3.0  2.3  2.2  1.8

81	82	C	4.7	H	  7.0  40.0  4.5  4.5

83	84	*	2.9	P	  41.5  75.0  8.5  7.2

85	86	-	4.3	M	  75.0  75.0  6.0  75.0

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