Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2bcqa1
---------------CCCCC-CHHHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCCCCC-CHHHHHHHHHHCCCCHHHHHC---

>P1;d2fmpa1
-------------CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHC

>P1;d4i2aa1
CCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCC--

>P1;d6ipna1
CCCCHHHCCCCCCCCCHHHHHHHHHHHHHHHHC-CCCC-CHHHHHHHHHHHHCCCCCCC-CCC-CCCCCC-CC-CCHHHHHHHCCCCHHHHHC--
PSA

>P1;d2bcqa1
---------------09600-204501711577-9478515906600820582855066-630480960b-810610220276740751683---

>P1;d2fmpa1
-------------a503601800540062047738459616615701710672778094082048174087811710622376870840492589

>P1;d4i2aa1
43666970938b724077005004210811787-96aa41570560040030075407638307c0220bb603500550278680a40727a--

>P1;d6ipna1
14586860925a91606a107004200622178-877c-35614500200201865087-a42-e1240c-60-5007512679503047457--


Translating the sequences
---------------C****-*HHHHHHHHHHC-CCHHHHHHHHHHHHHHH*CCCCCCC-****CCCCCC-*HHHHHHHHHH*CCC*HHHH*---
-------------CCCHHHHHHHHHHHHHHHHC*CCHHHHHHHHHHHHHHH*CCCCCCC*****CCCCCC**HHHHHHHHHHHCCC*HHHH****
*************CCCHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHH*CCCCCCC*****CCCCCC**HHHHHHHHHHHCCC*******--
*************CCCHHHHHHHHHHHHHHHHC-CC**-*HHHHHHHHHHH*CCCCCCC-***-CCCCCC-**-**HHHHHHHCCC*HHHH**--

47802.tem
_________________________________
*************CCCHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHH*CCCCCCC*****CCCCCC**HHHHHHHHHHHCCC*HHHH**--




Structural block scores
0	12	*	3.5	M	  75.0  75.0  6.1  5.7

13	15	C	4.5	M	  50.0  5.2  2.0  2.3

16	31	H	4.7	H	  7.7  2.9  3.2  3.0

34	35	C	5.0	H	  6.5  6.0  7.5  7.5

36	50	H	4.8	H	  4.1  4.1  3.7  8.2

52	58	C	5.0	H	  4.6  5.3  4.1  5.0

59	63	*	1.8	P	  17.6  2.8  4.2  33.3

64	69	C	5.0	H	  5.8  4.7  4.7  5.7

70	71	*	2.2	P	  41.5  7.5  8.8  40.5

72	82	H	4.7	H	  2.5  3.3  3.2  9.8

83	85	C	5.0	H	  3.7  5.0  4.7  4.7

87	90	H	4.3	M	  5.0  4.2  3.2  3.8

91	92	*	1.6	P	  39.0  3.5  8.8  6.0

93	94	-	4.3	M	  75.0  8.5  75.0  75.0

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