CMD - Cotton Marker Database
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The input to the primer redundancy package is a fasta file (.fasta extension) containing the set of sequences that needs to be checked for redundancy. This analysis tool is built around the pairwise comparison algorithm with the restriction of no gap and no mismatch. MON SSR project data was not included in the primer redundancy analysis due to the lack of data on target repeat motifs.

View redundancy analysis output:
CMD Pimer sequences
Input Fasta file
List of redundant sequences

Processing Summary
Number of primer sequences analyzed (forward and reverse) 18,002
Total number of redundant primer sequences found 2,570
Total number of non-redundant primer sequences 15,432
Threshold value for the analysis 0.81 (81%)
Total number of redundant primer pairs 1,422
Total number of completely matched sequence pairs (match percentage 100) 940
Total number of closely matched sequence pairs (match percentage 90-99) 280
Total number of closely matched sequence pairs (match percentage 81-89) 202
Type of primer sequence match (pairs):
Forward-forward match 460
Reverse-reverse sequence match 414
Forward-reverse sequence match 232
Reverse-forward sequence match 316
Both forward-forward and reverse-reverse match 103
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