Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1loua-
----CEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEEEEEECCEEEEEEEEEEEEEC-HHHHHHHHHHHHCCCCEEEEEEEECC--CCC-----

>P1;d1vmba-
----CEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC-CCCEEEEEEEEEEEC-CCCCHHHHHHHHCCCCEEEEEEEECHHHHHHHCCCC

>P1;d2j5aa1
CCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCEEEEEEEEEEEEECCCCCCCCCEEEEEEEEEEECCCCHHHHHHHHHHHCCCEEEEEEEEECHHHCCCC---

>P1;d2qalf1
----CCEECEEEEECHHHHH-HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECC-HHHHHHHHHHCCCCCCEEEEEECCCC--CCCCCCC-
PSA

>P1;d1loua-
----453120300020707a8517603820471057270601335333568087426835402101000202-69419500640573b30120515609--946-----

>P1;d1vmba-
----6400101000018166961460065026204660701462323625709a73-737300100020307-064363037106817500522262276217846889

>P1;d2j5aa1
a955241110200011616696057106501710583a0711043356458099536a28500101000307477028404750553930042414508695169a---

>P1;d2qalf1
----4611302010309318-30680196127807a490622122443568097528636501100000203-67117614760594c00150425726--9256973-


Translating the sequences
----CEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCC***EEEEEEEEE*****CC**EEEEEEEEEEEC-**HHHHHHHHHHCCCCEEEEEEEECC--*CC-----
----CEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCC***EEEEEEEEECCCCC-CCCEEEEEEEEEEEC-****HHHHHHHHCCCCEEEEEEEEC*******C***
****CEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCC****EEEEEEEEECCCCCCCCCEEEEEEEEEEEC***HHHHHHHHHH*CCCEEEEEEEE*C***CC*C---
----C*EE*EEEEEC****H-HHHHHHHHHHHHHHHCCC************CCCCCCCCC********EE*C-**HHHHHHHH**CCCCEEEEEE**CC--*CC*C**-

54995.tem
_________________________________
----CEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCC***EEEEEEEEECCCCCCCCCEEEEEEEEEEEC-**HHHHHHHHHHCCCCEEEEEEEECC***CC*C**-




Structural block scores
0	3	-	4.3	M	  75.0  75.0  7.4  75.0

5	13	E	4.8	H	  1.6  0.7  1.0  1.6

14	18	C	4.4	M	  3.2  3.2  3.0  3.2

19	35	H	5.0	H	  4.4  3.7  3.9  8.9

36	38	C	4.8	H	  3.0  4.3  4.5  4.3

39	41	*	1.0	P	  2.3  1.7  3.0  3.3

42	50	E	4.3	M	  4.3  4.0  4.2  3.9

51	59	C	4.4	M	  4.8  13.5  5.8  5.1

60	70	E	4.4	M	  0.9  0.8  0.9  0.8

73	74	*	1.0	P	  7.5  3.0  7.0  6.5

75	84	H	4.7	H	  3.4  3.3  3.5  3.8

85	88	C	4.8	H	  6.1  5.2  5.0  6.4

89	96	E	4.8	H	  2.5  2.4  2.5  3.0

97	98	C	4.3	M	  4.5  4.5  4.0  4.0

99	101	*	2.7	P	  53.0  3.0  6.7  53.0

102	103	C	4.3	M	  5.0  7.5  3.5  3.5

106	107	*	3.5	M	  75.0  8.0  75.0  5.0

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