Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2ooja1
C-CEEEEEEECCCCCCCCCCCCCCCCCCC-CEEEEECCCCCE-EEEE-EEECCCCCCEEEEEEEEEECCCCCEEEEEEEEECCC----CEEEEECCCCCEE-CCCCC-CEEEEEC--CCEEEEEECCCC

>P1;d2q03a1
CCCEEEEEEEEEEEEEEEEEC--CCEEEEEEEEEEECCCEEEEEEEEEEEEEECCEEEEEEEEEEEEEEC-CCEEEEEEEEEEECCEEEEEEEEC-CCCC-HHHCCCCCCEEEECCCCEEEEEEECCC-
PSA

>P1;d2ooja1
b-6817450615783a1b7909c73b263-316150595080-0845-634479913275160506203c4722021615137b----836140379206a-70780-3583758--b3330304052b

>P1;d2q03a1
874417704256482925666--b4240403040108a7062807060541669750616360507450d-3410205080634a8533080604-a206-9704a0713505348965080305056-


Translating the sequences
C-CEEEEEEE**********C**CC****-*EEEEECCC**E-EEEE-EEE**CC**EEEEEEEEEE**C*CEEEEEEEEE***----*EEEEEC*CCCE*-**CCC-CEEEEEC--C*EEEEEECCC*
C*CEEEEEEEEEEEEEEEEEC--CCEEEE*EEEEEECCCEEE*EEEE*EEEEECCEEEEEEEEEEEEEEC-C*EEEEEEEEEEE****EEEEEEC-CCC*-*HHCCC*C*EEEEC**CEEEEEEECCC-

159238.tem
_________________________________
C-CEEEEEEEEEEEEEEEEEC--CCEEEE-EEEEEECCCEEE-EEEE-EEEEECCEEEEEEEEEEEEEEC-CEEEEEEEEEEEE----EEEEEEC-CCCE--HHCCC-CEEEEEC--CEEEEEEECCC-




Structural block scores
3	19	E	3.8	M	  5.5  4.6

21	22	-	3.0	P	  10.8  75.0

23	24	C	5.0	H	  5.0  7.8

25	28	E	3.0	P	  5.6  2.5

30	35	E	4.7	H	  2.7  1.3

36	38	C	5.0	H	  6.3  8.5

39	41	E	3.7	M	  2.7  2.7

43	46	E	5.0	H	  4.2  3.2

48	52	E	4.2	M	  4.8  4.4

53	54	C	5.0	H	  9.0  8.0

55	68	E	4.4	M	  2.9  3.4

72	83	E	4.3	M	  3.5  2.8

84	87	-	3.0	P	  75.0  6.6

88	93	E	4.7	H	  3.7  2.8

96	98	C	5.0	H	  3.7  4.2

100	101	-	3.0	P	  42.8  42.0

102	103	H	3.0	P	  3.5  3.5

104	106	C	5.0	H	  5.0  4.8

109	113	E	4.6	H	  5.6  3.2

115	116	-	3.0	P	  75.0  8.5

118	124	E	4.7	H	  2.3  3.0

125	127	C	5.0	H	  2.3  3.7

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