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mature miRNA: CATGTGCCCATCTTCCCCATC
species: Cichorium intybus
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|218979104|gb|FL676036.1|FL676036 CIRGL006H11 CiRG Cichorium intybus cDNA 3', mRNA sequence 

CATGTGCCCATCTTCCCCATC
|||.||||||| || ||||||
GTATACGGGTAAAATGGGTAG

EST sequence (targeted fragment marked with yellow):
TTTCGTTCGAGAAAATTTGGGACGGGGTTTTGAGTGGTATGGAGCGGTGTATGGAGGTTAAGTTTAGAGGGAAACGAAGCGAGAAAATTTACGAGTTAGTCCCTGAGCTTTTGAAGAACACTTTGCTTGTCATGAAGTCGAACGGAATCCTTCATTCCGGCGGTGATTCCGATTCCGATGGCGATGGGGTATGGAATCAGACTTGGGTACATATGAAAACACTAGCACCTTCGTTGCGGTCGGAGGTGTTCCCGGATGATGAACCGGAACCAGGACCGCAGACCATGGGTGCGGACCCGGTTCCGGAGGCAAACCTATTGGTTCCTTGAAATTTTTGATGGGTAAAATGGGCATATGAGAATGGTTAAGTTTTTAGTTGAGGAGGTTTTTCATATATTTGTATACTTTTAGTAGATTTGTATAATTGTTGGTTTGAGATGAACCATGATGAACAAGTGTTTTTTTTTTTCTTGGTTTTGGTTTTGGTTTGACTTTGACTTTTGACATTTGTTGCCCTTTTGACCCATCGAAGGGATTTATATGGAGTCACCCAGATT