Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1akya2
CEEECCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCC

>P1;d1zaka2
CEEECCCCCCEEECCCCCCCCC----HHHHHCCCC---

>P1;d1zina2
CEEEECCCCCEEECCCCCCCCCCCCCCCCCCEECC---
PSA

>P1;d1akya2
43010463744125889509596502857670574b72

>P1;d1zaka2
45340463747035789517b7----815830677---

>P1;d1zina2
35210563625024776508888505636160367---


Translating the sequences
CEEECCCCCCEEECCCCCCCCCCCCCCCCCCCCCC***
CEEECCCCCCEEECCCCCCCCC----*****CCCC---
CEEE*CCCCCEEECCCCCCCCCCCCCCCCCC**CC---

57774.tem
_________________________________
CEEECCCCCCEEECCCCCCCCCCCCCCCCCCCCCC---




Structural block scores
1	3	E	5.0	H	  1.3  4.0  2.7

4	9	C	4.8	H	  4.0  4.0  3.7

10	12	E	5.0	H	  2.3  3.3  2.3

13	34	C	4.5	M	  5.5  18.4  5.0

35	37	-	4.0	M	  6.8  75.0  75.0

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