Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1ni3a2
CEEEEECC--CCCCEEEEEC-CCCCHHHHHHHHCHHHHHCCCEEECC-HHHHHHHCCHHHHHHCCCCCEEECCCC-CCCCCCCCC--

>P1;d1nyra2
-CCCCCCCCC-----CCCCC-CCCCHHHHHHCCCHHHHHHCCEEEECC-------------------EEECCCCCCCCCCCCCEE--

>P1;d1tkea1
CCEEECCCCC-----EEECC-CCCCHHHHHHHHCHHHHHHCCEEEECC-------------------EEEECCCCCCCCEEEEEECC

>P1;d1wxqa2
CCEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHCHHHHHCEEEEEECCCC-----------------CCCCCCCCCCCCEEEEEEEC

>P1;d2dbya2
CEEEEEEC--CCCEEEEEEC-CCCCHHHHHHHHCCC-CCCCCEEEEEEHHHHHHHCCHHHHHHCCCCEEECCCCCCCCCEEEEEE-C
PSA

>P1;d1ni3a2
61303239--bb76541518-88240050004177824890851302-6713653755a40583a4135246816-562020408--

>P1;d1nyra2
-150415678-----4680a-652204500554559337908204057-------------------960817650585350514--

>P1;d1tkea1
7020206886-----53717-72000350065249b309606204168-------------------8527185506a707040439

>P1;d1wxqa2
02031169369b89427539977220350046476830720530210578-----------------851a5a37086502020208

>P1;d2dbya2
60303224--b776551509-66040170005199b-4aa055010036531760472970585920442569160761000612-9


Translating the sequences
C*EEEECC--CCC**EEE*C-CCCCHHHHHHHHCHHHHHCCCEEE*C-********************EE*CCCC-CCC******--
-C****CCCC-----***CC-CCCCHHHHHH**CHHHHH*CCEEEECC-------------------EEECCCCCCCCC****EE--
CCEEE*CCCC-----EEECC-CCCCHHHHHHHHCHHHHH*CCEEEECC-------------------EEE*CCCCCCCCEEEEEE*C
CCEEEECCCCCCC*****CC*CCCCHHHHHHHHCHHHHHC**EEEECC**-----------------***CCCCCCCCCEEEEEE*C
C*EEEE*C--CCC**EEE*C-CCCCHHHHHHHHC**-**CCCEEEE*********************EEECCCCCCCCCEEEEEE-C

81271.tem
_________________________________
CCEEEECCCCCCC**EEECC-CCCCHHHHHHHHCHHHHHCCCEEEECC**-----------------EEECCCCCCCCCEEEEEE-C




Structural block scores
0	1	C	4.2	M	  3.5  38.0  3.5  1.0  3.0

2	5	E	4.3	M	  2.0  2.5  1.0  1.2  2.0

6	12	C	4.4	M	  27.4  35.9  36.1  7.5  25.9

13	14	*	3.0	P	  5.5  75.0  75.0  6.5  5.5

15	17	E	3.8	M	  3.3  6.0  5.0  4.7  3.7

18	19	C	4.4	M	  4.5  5.2  4.0  6.0  4.5

21	24	C	5.0	H	  5.5  3.8  2.2  4.5  4.0

25	32	H	4.9	H	  1.2  2.9  2.6  2.8  1.8

34	38	H	4.5	M	  5.8  5.4  6.5  4.8  22.0

39	41	C	4.3	M	  5.7  5.7  4.0  2.3  5.2

42	45	E	4.9	H	  2.2  1.5  1.8  1.5  1.5

46	47	C	4.3	M	  38.5  6.0  7.0  2.5  1.5

48	49	*	3.0	P	  6.5  75.0  75.0  7.5  5.5

50	66	-	3.8	M	  4.8  75.0  75.0  75.0  4.4

67	69	E	4.3	M	  3.3  5.0  5.0  4.7  3.3

70	78	C	4.8	H	  12.6  5.0  5.5  6.1  4.6

79	84	E	4.0	M	  2.3  3.0  2.5  1.0  1.5

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