Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1q90m-
CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC

>P1;d4ogqf-
-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-
PSA

>P1;d1q90m-
99a8779678667856779766787777686688

>P1;d4ogqf-
-baba8777676886785788779566686795-


Translating the sequences
*HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC*
-**HHHHHHHHHHHHHHHHHHHHHHHHHHHH*C-

103441.tem
_________________________________
-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-




Structural block scores
1	31	H	4.8	H	  7.1  7.5

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