Kindly see the attached file. Hope it will solve your purpose. 

/*test data set: diploid*/

Number of Populations = 3

Number of Loci = 5

Locus name:

locus1  locus2  locus3  locus4  locus5

name = 1

AA   BB   AB   BC  CC

name = 1

AB  BC  CC  BB  AA

name = 3

BB  AA  AC  BC  AC

yes, keep the correct data style is important, 

Pear use CONVERT software for conversion of files to different Population genetic softwares

Yes, it is important to enter data is correct format and style

You can also use GenAlEx, where you can export your input file in format for popgene analysis. 

Thank you very much you all,,, finally, I got it..!!

Analysis of co-dominant marker data set by Popgene software utilizes genotypic information (homozygous or heterozygous nature) based data set similar to that required for analysis by Power Marker software.

Is there any r based analysis with popgene analysis