Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2j98b-
----CCCCEEEEEEEEEEHHHC--EEEEEEEEEECCCCEEEEEEEECCCCEEEEEEECCCCE--EEEECCCCEEEEECCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHC---

>P1;d5ym6a-
--CCCCCEEEEEEEEEECCCCC--EEEEEEEEEE--CCCEEEEEEECCCCC-CEEEECCCCE--EEECCCCCEEC---------CCEEEECCCCCHHHHHHHHHHHCC-----

>P1;d7kria1
CCCCCCCCCEEEEEEEECCCCCCCCCCEEEEEEEECCEEEEEEEEECCCCCCEEECCHHHCCCCCCEECCCCEEEEEEECCEEEEEEEEECCCCCHHHHHHHHHHHHHHCCCC
PSA

>P1;d2j98b-
----73a805247250109cb5--40835001042bb624000010745705305061b875--6616028276261829967442100104b06a8327206a319843---

>P1;d5ym6a-
--a8883707277140209988--6460500003--ca4500000183650-301064ba97--46370282675---------54210005a079723830694288-----

>P1;d7kria1
bb8a7968366250000674a507a5403010555a91360000104559052030498073b87223027266222229965531100014b08a83277059715873836


Translating the sequences
----CCCCEEEEEEEEE****C--EEEEEEEEEE*CCCEEEEEEEECCCC**EEEEECCCCE--EEEECCCCEEEEE**CC**EEEEEEECCCCCHHHHHHHHHHHHHHC---
--CCCCC*EEEEEEEEECCCCC--EEEEEEEEEE--CC*EEEEEEECCCCC-*EEEECCCCE--EEE*CCCCEE*---------**EEEECCCCCHHHHHHHHHHH**-----
**CCCCCC*EEEEEEEECCCCC*****EEEEEEE*CC*EEEEEEEECCCCC*EEE*****C*****EECCCCEEEEE**CC**EEEEEEECCCCCHHHHHHHHHHHHHHC***

101816.tem
_________________________________
--CCCCCCEEEEEEEEECCCCC--EEEEEEEEEE*CCCEEEEEEEECCCCC*EEEEECCCCE--EEEECCCCEEEEE**CC**EEEEEEECCCCCHHHHHHHHHHHHHHC---




Structural block scores
0	1	-	4.0	M	  75.0  75.0  11.5

2	7	C	4.5	M	  29.8  7.4  8.1

8	16	E	4.9	H	  2.9  3.3  2.4

17	21	C	4.2	M	  7.6  6.8  6.5

22	23	-	4.0	M	  75.0  75.0  3.5

24	33	E	4.7	H	  2.5  2.4  3.4

35	37	C	4.3	M	  9.7  32.7  6.8

38	45	E	4.9	H	  0.9  1.2  1.2

46	50	C	4.8	H	  4.6  4.4  4.6

52	56	E	4.4	M	  2.8  2.0  1.8

57	60	C	4.2	M	  6.9  8.8  6.0

62	63	-	4.0	M	  75.0  75.0  9.8

64	67	E	4.2	M	  4.8  5.0  3.5

68	71	C	5.0	H	  3.0  3.0  2.8

72	76	E	4.4	M	  4.4  33.6  3.6

77	78	*	2.7	P	  5.0  75.0  2.0

79	80	C	4.0	M	  9.0  75.0  9.0

81	82	*	2.7	P	  6.5  75.0  5.5

83	89	E	4.6	H	  1.7  12.4  1.4

90	94	C	5.0	H	  4.3  4.5  4.9

95	108	H	4.8	H	  5.3  10.3  5.7

110	112	-	4.0	M	  75.0  75.0  5.7

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