Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2dpya1
CC-CCEEEEECCCCCEEEECCC--CCCCCEEEEEECCCCCCEEEEEEEEECCC-CCEEEEECCCCCCCCCCEEEEEC---

>P1;d2jdia2
CCCCEEEEEEEECCEEEEEECC-CCCCCCEEEECC-------CCEEEEEEECC-CCEEEEECCCHHHCCCCCEEECCCCC

>P1;d2jdid2
---CEEEEEEEECCEEEEEECCCCCCCCCEEEECCCC----CCCEEEEEEEEECCEEEEEECCCCCCCCCCCEEEECCCC

>P1;d3gqba1
--CCEEEEEEEECCEEEEECCCC-CCCCCEEEECC-C-----CEEEEEEEEEC-CEEEEEECCCCCCCCCCCEEEECCCC

>P1;d3ssaa1
-----------CCCEEEEECCC-CCCCCCEEEEECC---CCCEEEEEEEEEC-CCEEEEEECCC-----CCEEEEC----
PSA

>P1;d2dpya1
b4-9216035469750203b09--1777330001345a88673050503367c-74030405594a80683150056---

>P1;d2jdia2
756420505717b440305006-508671303063-------62303046339-91000305773750876240624b3b

>P1;d2jdid2
---650303419c740103068920657010203c1a----97010304632ab510405047709a0887270514866

>P1;d3gqba1
--93704046179550105608b-06450205008-8-----3140204537a-810304056909b0876240302386

>P1;d3ssaa1
-----------45741606175-90a754402051b---7665350202817-a86020203bc-----c506162----


Translating the sequences
**-C*EEEEE**CC*EEEECCC--CCCCCEEEE**CC******EEEEEEE*CC-C*EEEEECCCCCCCCCC*EEEEC---
***CEEEEEEEECCEEEEE*CC-CCCCCCEEEECC-------C*EEEEEEECC-C*EEEEECCC***CCCCCEEE*CCCC
---CEEEEEEEECCEEEEE*CC*CCCCCCEEEECCCC----*C*EEEEEEE***CEEEEEECCCCCCCCCCCEEEECCCC
--*CEEEEEEEECCEEEEECCC*-CCCCCEEEECC-C-----CEEEEEEEE*C-CEEEEEECCCCCCCCCCCEEEECCCC
-----------*CCEEEEECCC-CCCCCCEEEE*CC---****EEEEEEEEC-*CEEEEEECCC-----CC*EEE*----

50615.tem
_________________________________
---CEEEEEEEECCEEEEECCC-CCCCCCEEEECCCC----*CEEEEEEEECC-CEEEEEECCCCCCCCCCCEEEECCCC




Structural block scores
0	2	-	3.8	M	  30.2  6.0  75.0  53.0  75.0

4	11	E	4.3	M	  3.4  3.4  3.1  3.6  66.1

12	13	C	5.0	H	  8.0  7.8  9.8  7.0  6.0

14	18	E	4.9	H	  2.0  2.4  1.6  2.2  3.4

19	21	C	4.6	H	  6.8  2.0  4.7  4.7  4.3

23	28	C	4.9	H	  16.7  4.5  3.3  15.0  5.9

29	32	E	5.0	H	  0.8  1.5  0.8  1.8  1.5

33	36	C	4.2	M	  3.2  39.8  6.8  22.8  23.1

37	40	-	4.2	M	  8.1  75.0  75.0  75.0  40.8

43	50	E	4.8	H	  2.8  2.6  2.1  2.4  2.6

51	52	C	3.9	M	  9.8  6.0  6.2  8.8  41.0

55	60	E	4.8	H	  1.8  0.7  1.7  1.3  1.7

61	71	C	4.6	H	  5.4  5.2  5.7  5.8  38.1

72	75	E	4.7	H	  2.5  3.0  3.2  1.8  3.8

76	79	C	4.3	M	  57.8  7.5  6.0  4.8  75.0

>>>>>>