Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1pj5a1
CEEEEEEEECCCCCCCCCCCEEEEC---C-EEEEECCCEEEECCCCEEEEEEEEECCC-CCCCEEEEEEC-CEEEEEEEECCCCCCCCCCCC---C

>P1;d1v5va1
-CEEEEEEECC-CCCCCCCCEEEEC---C-EEEEEEEEEEECCCCCCEEEEEEECHHHCCCCCEEEEEEC-CEEEEEEEECCCCCCCCCCCCCCCC

>P1;d1vloa1
CCEEEEEECC--CCCCCCCCEEEEECCCCCEEEEEEEEEEEECCCCEEEEEEEECCCC----CEECCCCCC---CCEEEECCCCEE----CCEECC

>P1;d1vlya1
CCCCEEEEECC-CCCCCCCCCCEECC---CCCCCEEEEEEECCC-CCEEEEEECCC---CCCCCEECC---CCCCCEEEECCC-CCC---------

>P1;d1wosa1
-CEEEEEEEC-CCCCCCCCCEEEEC---C-EEEEEEEEEEEECCCCEEEEEEEECCCC-CCCCEEEEEECCCEEEEEEEECCCCC---CCCC---C
PSA

>P1;d1pj5a1
a464100004548340729140128---8-85216039082297373020205023a0-65736030239-783050403846162497877---f

>P1;d1v5va1
-5660304044-a33068824000a---7-6401404706508428402130304562065828030308-944250202734145567348858c

>P1;d1vloa1
b454000169--9450778130515198779251403605508516301030502a0a----96030427b---661703844127----9b853b

>P1;d1vlya1
a7233401350-9540877220044e---c264350470755b9-75030403959---88a251104---709640514816-6a6---------

>P1;d1wosa1
-744000107-a854078714022a---8-8502302708317626502030305980-76717030206b77518040285426---74b9---a


Translating the sequences
C*EEEEEEECC*CCCCCCCCEEEEC---C-EEEEE***EEEECCCCEEEEEEEE*CCC-CCCCEEEEEEC-CEEEEEEEECCCCCCC*CCCC---C
-CEEEEEEECC-CCCCCCCCEEEEC---C-EEEEEEEEEEE*CCCC*EEEEEEEC****CCCCEEEEEEC-CEEEEEEEECCCCCCC*CCCC***C
CCEEEEEE*C--CCCCCCCCEEEE****C*EEEEEEEEEEEECCCCEEEEEEEECCCC----CEE****C*---**EEEECCCC**----CC***C
CC**EEEEECC-CCCCCCCC**EEC*---*****EEEEEEE*CC-C*EEEEEE*CC---CCCC*EE**---C****EEEECCC-CCC---------
-CEEEEEEEC-*CCCCCCCCEEEEC---C-EEEEEEEEEEEECCCCEEEEEEEECCCC-CCCCEEEEEEC*CEEEEEEEECCCCC---CCCC---C

101790.tem
_________________________________
CCEEEEEEECC-CCCCCCCCEEEEC---C-EEEEEEEEEEEECCCCEEEEEEEECCCC-CCCCEEEEEEC-CEEEEEEEECCCCCCC-CCCC---C




Structural block scores
0	1	C	4.3	M	  7.2  40.0  7.8  8.8  41.0

2	8	E	4.8	H	  1.6  2.7  2.3  2.3  1.3

9	10	C	4.6	H	  4.5  4.0  42.0  2.5  41.0

12	19	C	5.0	H	  4.2  5.1  5.1  5.2  5.0

20	23	E	4.8	H	  1.8  1.0  2.2  1.5  2.0

25	27	-	4.3	M	  75.0  75.0  6.0  54.8  75.0

30	41	E	4.6	H	  3.8  3.1  3.3  4.0  3.2

42	45	C	4.9	H	  6.5  5.5  5.0  25.6  5.2

46	53	E	4.8	H	  1.5  1.6  1.5  3.0  1.6

54	57	C	4.3	M	  3.9  4.2  5.8  41.0  5.5

59	62	C	4.6	H	  5.2  5.2  58.5  7.1  5.2

63	68	E	4.3	M	  2.3  2.3  2.5  14.3  2.0

72	79	E	4.5	M	  2.9  2.4  21.6  3.6  3.4

80	86	C	4.6	H	  4.4  4.1  14.4  16.1  25.0

88	91	C	4.3	M	  7.2  5.5  42.6  75.0  7.9

92	94	-	3.8	M	  75.0  7.0  5.3  75.0  75.0

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