Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1g4wr1
-------------CHHHHHHHHHCCHHHHHCCCCHHHC-----------CHHHHHHHHHHHCC-----HHHHHHHHHHCCCCCCCCHHHC-----CHHHHHC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHCC--

>P1;d1he1a1
CHHHHHHHHHHHHCHHHHHHHHH-HHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCEECCEEHHHHCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC

>P1;d1hy5a-
-------CCHHHHHHHHHHHHCC-CCCCHHHCCCC-CCCCHHHHCCCCCHHHHHHHHHHHC-CCCCH-HHHHHHHHHHHCEECCEEHHHHHCCCCHHHHHHCCCC--CCHHHHHHHHHHHHC-CHHHHC------
PSA

>P1;d1g4wr1
-------------65a8017204600460381808503-----------62930160073067-----9227406811646019040250-----6189218-067850550064037008404501650577--

>P1;d1he1a1
a9977775663383047118405-6085059061810272085006c7200410180053065006578035202700736008130550043b77037308706692246004203601740760285057238

>P1;d1hy5a-
-------7575652476067315-50740580737-0675067206872004110510540-8507c-8157205601845019130250063975027217585--806600630280262-650373------


Translating the sequences
-------------CHHHHHHHHH*CHHHHH*CCCHHHC-----------*HHHHHHHHHHH*C-----HHHHHHHHHHCC**CC**HHH*-----*HHHHHC-CCHHHHHHHHHHHHHHHHHHHHHHHHHH**--
*********HHHHCHHHHHHHHH-*HHHHHHCC*HHH***HHHHCCCCCHHHHHHHHHHHH***CC**HHHHHHHHHHCCEECCEEHHHH*CCCCHHHHHH**CCHHHHHHHHHHHHHHHHHHHHHHHHHH****
-------**HHHH*HHHHHHH**-C***HHHCCC*-*C**HHHHCCCCCHHHHHHHHHHH*-C*CC*-HHHHHHHHHH*CEECCEEHHHH*CCCCHHHHHHC*CC--**HHHHHHHHHHHH*-*HHHH*------

47233.tem
_________________________________
-------**HHHHCHHHHHHHHH-CHHHHHHCCCHHHC**HHHHCCCCCHHHHHHHHHHHH*C*CC*-HHHHHHHHHHCCEECCEEHHHH*CCCCHHHHHHC*CCHHHHHHHHHHHHHHHHHHHHHHHHHH**--




Structural block scores
0	6	-	4.0	M	  75.0  8.1  75.0

7	8	*	2.7	P	  75.0  5.5  6.0

9	12	H	4.0	M	  75.0  5.0  5.8

14	22	H	4.8	H	  4.2  3.3  4.3

25	30	H	4.3	M	  3.5  4.5  4.0

31	33	C	4.7	H	  3.0  2.3  3.3

34	36	H	4.0	M	  4.3  3.0  27.3

38	39	*	2.7	P	  75.0  4.5  6.0

40	43	H	4.0	M	  75.0  3.2  3.8

44	48	C	4.0	M	  75.0  5.5  4.6

49	60	H	4.8	H	  3.1  1.8  1.8

64	65	C	4.0	M	  75.0  3.0  3.5

68	77	H	5.0	H	  4.0  2.7  3.5

78	79	C	4.5	M	  5.0  5.0  6.0

80	81	E	4.0	M	  3.0  3.0  2.5

82	83	C	5.0	H	  5.0  4.0  5.0

84	85	E	4.0	M	  2.0  2.0  2.0

86	89	H	4.8	H	  1.8  2.5  1.8

91	94	C	4.0	M	  75.0  6.4  6.2

95	100	H	4.8	H	  4.5  3.3  2.8

103	104	C	5.0	H	  3.0  3.0  6.5

105	130	H	4.6	H	  3.4  3.4  17.2

131	132	*	2.7	P	  7.0  4.5  75.0

133	134	-	4.0	M	  75.0  5.5  75.0

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