Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2fj6a1
CCCHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCHHHHCCHHHHHHHHHHHHHHHCCC

>P1;d2o6ka1
-CCHHHHC-CCCC--CCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCC-CCCCHHHHHHHHHHHHHHC-
PSA

>P1;d2fj6a1
74101510493647a37672060026167287122a515597025305838806a32a1075018706651897

>P1;d2o6ka1
-7002500-704b--4a5520600430573970259466496038128660a0-8077116501730373489-


Translating the sequences
*CCHHHHH*HCCC**CCCHHHHHHHHHH*CCCCCCCCCCHHHHHHHHHH*HHH*CCHHHHHHHHHHHHHHH*C*
-CCHHHH*-*CCC--CCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHH***-CC**HHHHHHHHHHHHHHC-

140652.tem
_________________________________
-CCHHHHH-HCCC--CCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHH-CCHHHHHHHHHHHHHHHHC-




Structural block scores
1	2	C	5.0	H	  2.5  3.5

3	7	H	4.6	H	  1.4  1.4

10	12	C	5.0	H	  4.3  5.2

13	14	-	3.0	P	  8.8  75.0

15	17	C	5.0	H	  5.3  6.5

18	28	H	4.8	H	  3.4  2.9

29	38	C	5.0	H	  4.3  5.1

39	52	H	4.4	M	  4.5  4.5

54	55	C	5.0	H	  6.8  4.0

56	71	H	4.6	H	  4.2  3.9

>>>>>>