Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1mgta2
-CEEEEEEEECCEEEEEEEEECCCEEEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCCCCC-----CCHHHHHHHHHCCCCCHHHHHHHCCCCC

>P1;d1sfea2
CCCEEEEEEECC-EEEEEEECCCCEEEEEEECCC-CHHHHHHHHCC---------CCEECCCCHHHHHHHHHHHHHHHCC---CCCCCCCCCCC

>P1;d3l00a1
CCCEEEEECCCC-CEEEEEEECCEEEEEEEEECCCCHHHHHHHHHHHHHHC---------HHHHHHCCCCCCCCHHHCC---------------
PSA

>P1;d1mgta2
-400044165ba6202000005c50023160665b3027506621850586a0a0725649-----2710531141438638a75067220752

>P1;d1sfea2
b90211138076-820000009720012144a75-70375058427---------a08627a4a8036206501612369---84819064085

>P1;d3l00a1
3a2652418056-650300009700153554a4694103301431605155---------592298367074145753a---------------


Translating the sequences
-C*EEEEEEECC*EEEEEEEECCCEEEEEEECC***HHHHHHHHHHHHHHC****CC**CC-----CCHHHHHHHHHCCC*********CCCCC
CCCEEEEEEECC-EEEEEEE*CCCEEEEEEECCC-CHHHHHHHH**---------CC**CC**HHH**HHHHHHHHH*CC---******CCCCC
CCCEEEEE**CC-*EEEEEEECC*EEEEEEE*CC*CHHHHHHHHHHHHHHC---------***HHHCC******HHHCC---------------

53155.tem
_________________________________
CCCEEEEEEECC-EEEEEEEECCCEEEEEEECCC*CHHHHHHHHHHHHHHC----CC**CC**HHHCCHHHHHHHHHCCC---******CCCCC




Structural block scores
0	2	C	4.3	M	  26.3  6.8  5.2

3	9	E	4.7	H	  2.9  2.3  3.7

10	11	C	5.0	H	  11.0  6.5  5.5

13	20	E	4.8	H	  0.5  1.2  1.8

21	23	C	4.7	H	  7.5  6.0  5.3

24	30	E	5.0	H	  1.7  1.7  3.3

31	33	C	4.3	M	  5.7  7.5  6.8

36	49	H	4.6	H	  3.9  24.4  2.4

51	54	-	4.0	M	  5.2  75.0  75.0

55	56	C	4.0	M	  4.5  5.2  75.0

57	58	*	2.7	P	  5.5  7.0  75.0

59	60	C	4.0	M	  6.5  4.5  40.0

61	62	*	2.7	P	  75.0  7.2  5.5

63	65	H	4.0	M	  75.0  6.2  6.3

66	67	C	4.0	M	  4.5  4.5  4.5

68	76	H	4.3	M	  2.2  2.6  4.4

77	79	C	4.3	M	  5.7  6.0  29.5

80	82	-	4.0	M	  7.2  75.0  75.0

83	88	*	2.7	P	  4.5  5.0  75.0

89	93	C	4.0	M	  3.2  4.6  75.0

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