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mature miRNA: GGAATGTTGTCTGGCTCGAGG
species: Theobroma cacao
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|212317334|gb|CU530930.1|CU530930 CU530930 TEGPULI_KZ0AAI_K Theobroma cacao cDNA clone KZ0AAK12YD16FM1, mRNA sequence

GGAATGTTGTCTGGCTCGAGG
|||||||||||||| ||.||.
CCTTACAACAGACCAAGTTCT

EST sequence (targeted fragment marked with yellow):
GATTTGATGAAGCTTCAAATCTTAAGTTGGGCTCTTTGTCTTCCACTAAGGCCTCCAAAAAAAATAAAAATGCAATTTAATGTACTTGTTTCCAAGACAAACATGAATTATTAGTGCCAAGAGGGCGAGATGATAGAGCCTCCTGCAAATCCAACAACTACCACCAGCAACAAGATGTAGCAAAATCCTTAATTTATATGTAGGATAGGAATTAGGAAACTAGTCAGCTTACTATTATTCTTCCTTTTGATTTCCCCGAGAGACCTGTAACTAACTGTTAAACTAATCATGCTACTGGTGATCGATGAAATCCAAGAATAAAACCACTGTACTTCCATGTAAAAATATTAAAAGTGGAAGCAGTAATTAAGGGGAATGAAGCCTGGTCCAAGAGCACAAATTAAACAGGGAATAAGACTATCTTTCGATTGATCTTGAAAGCTAATCAGTTTTTAGGCTCGAAACAGATCAAAATAGATGGAGAGTTGGGTGCTCTTGAACCAGACAACATTCCCCTCAACAAGAAAAGCTTCCCACCTGGAAACTATCTTCCTTGATCTTCCTTCTTCACTTTTCCGTTATTCTTTCCTTCAATACAACAATTCTTTTGCGGGTTTCGTGTGATATATTGTTGATGACGATGAACATAATCATTTGATTTTACGAGAGAAAGTAAAAGCGGTGAAAGAGAGAGATTGAGGAAGAACATGGGGGTCCCGAGGTCGTGGTCATTTCTGGAACCCAGCTGTTGGGTTGGGTTCAGCCCTGTTCTTTTTCTCTAACTTTTGGAACTCTAAATAATAAGCAAATCCTGTAAAAAACTGCCCAATCCCCGCGTACTCTG