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mature miRNA: GGAGCATCACCTGTTCTGAAA
species: Trifolium pratense
database: miRNEST
The numbers on the right side of the alignments show a score calculated for them.
When calculating the score, a mismatch is given a score of 1, bulge: 2, and wobble: 0.5.

Predicted miRNA targets
gi|86110629|gb|BB921838.1|BB921838 BB921838 Trifolium pratense leaf Trifolium pratense cDNA clone RCE28060, mRNA sequence 

GGAGCATCACCTGTTCTGAAA
|||||||||||||||||||||
CCTCGTAGTGGACAAGACTTT

EST sequence (targeted fragment marked with yellow):
TGATTGGAAAGAGTAATAAAGGAATGAAAATTACTTGCCAAGCTACTAGCATTCCTGCTGATAGAGTACCTGACATGAGTAAGAGGAAGACCTTGAATCTGCTTCTTCTTGGTGCTCTTTCACTTCCTACCGCTGGAATGCTTGTTCCTTATGGATCTTTCCTTGTCCCTCCAGGGTCAGGCTCTGCAACCGGTGGTACCGTTGCCAAGGATGCCGTTGGCAATGATGTAGTTGCAGCAGAATGGCTCAAGACTCATGGACCAGGCGACCGCACTCTTACCCAAGGATTAAAGGGTGATCCTACCTACCTTGTGGTAGAGAACGACAGAACACTTGCAACATTTGCGATTAATGCCGTATGCACTCACCTCGGGTGTGTCGTGCCGTTTAACACAGCTGAAAAAAAGTTCATCTGCCCATGCCATGGATCTCAGTACAATGACCAAGGAAGAGTTGTAAGAGGACCCGCTCCCTTGTCCCTTGCATTGGCACATTGTGATGTTGGTTTAGATGATGGGAAGGTTCTGTTTGTTCCATGGACTGAAACAGATTTCAGAACAGGTGATGCTCCATGGTGG


gi|86094765|gb|BB905974.1|BB905974 BB905974 Trifolium pratense three week-old plant Trifolium pratense cDNA clone RCE04125, mRNA 

GGAGCATCACCTGTTCTGAAA
|||||||||||||  ||||||
CCTCGTAGTGGACCTGACTTT

EST sequence (targeted fragment marked with yellow):
CGACCGCACTCTTACCCAAGGATTAAAGGGTGATCCTACCTACCTTGTGGTAGAGAGCGACAGAACACTTGCAACATTTGCGATTAATGCCGTATGCACTCACCTCGGGTGTGTCGTGCCGTTTAACACAGCTGAAAAAAAGTTCATCTGCCCATGCCATGGATCTCAGTACAATGACCAAGGACGAGTTGTAAGAGGACCCGCTCCCTTGTCTCTTGCATTGGCACATTGTGATGTTGGTTTAGATGATGGGAAGGTTTTGTTTGTTCCATGGAGCATCACCTGTTCTGAAATCTGTTTCAGTCCAGGTGATGCTCCATGGTGGTCTTAGACTTCTTAAACATGTCCCTATATTGTAATATATATTCAAATCTGAAATTCAAACATCTGTTTTTGTATTAATGCATAAACACATTTTGTAATCAAATCAATATTGTGTATTGAAGCTGGTATAAGGTGAAAACAAAACCTAGATGTTGTTTTTTTGTCCAT


gi|86104346|gb|BB915555.1|BB915555 BB915555 Trifolium pratense leaf Trifolium pratense cDNA clone RCE20850, mRNA sequence 

GGAGCATCACCTGTTCTGAAA
|||||||||||||||||||||
CCTCGTAGTGGACAAGACTTT

EST sequence (targeted fragment marked with yellow):
ATGATTGGAAAGAGTAATAAAGGAATGAAAATTACTTGCCAAGCTACTAGCATTCCTGCTGATAGAGTACCTGACATGAGTAAGAGGAAGACCTTGAATCTGCTTCTTCTTGGTGCTCTTTCACTTCCTACCGCTGGAATGCTTGTTCCTTATGGATCTTTCCTTGTCCCTCCAGGGTCAGGCTCTGCAACCGGTGGTACCGTTGCCAAGGATGCCGTTGGCAATGATGTAGTTGCAGCAGAATGGCTCAAGACTCATGGACCAGGCGACCGCACTCTTACCCAAGGATTAAAGGGTGATCCTACCTACCTTGTGGTAGAGAACGACAGAACACTTGCAACATTTGCGATTAATGCCGTATGCACTCACCTCGGGTGTGTCGTGCCGTTTAACACAGCTGAAAAAAAGTTCATCTGCCCATGCCATGGATCTCAGTACAATGACCAAGGAAGAGTTGTAAGAGGACCCGCTCCCTTGTCCCTTGCATTGGCACATTGTGATGTTGGTTTAGATGATGGGAAGGTTCTGTTTGTTCCATGGACTGAAACAGATTTCAGAACAGGTGATGCTCCATGGTGGTCTTAGACTTCTTAAACATGTCCCTATATTGTAATATATATTCAAATCTGAA