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mature miRNA: TGCCAAAGGAGAGTTGCCCTG
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|212100042|gb|CU541875.1|CU541875 CU541875 CORTINS_KZ0AAV Theobroma cacao cDNA clone KZ0AAV6YM18FM1, mRNA sequence 

TGCCAAAGGAGAGTTGCCCTG
 .||||||.||||||| ||||
TTGGTTTCTTCTCAACAGGAC

EST sequence (targeted fragment marked with yellow):
CGGGGGCATCAACCATATTCCCATCTCCCAAATCTTCTTTTCTTCTTTTATTTTGTCTTTCTTATTCTAATCTCATTTTCTTTCACTTTTATTCCTTCGAGAAAAAAACACAAACACTTTAAAGAAATATGTTAGTTTCAGAAACTTCCCTTTACAATCTTTAACATCCCCTCTTTCTCTCTCCAGGATTCTGTGTTGTTTTTATTCTTTTGTCTCAGAAAGAGAGAGAGCAGATAAAAAAGCTTGTAAGTGAGCTAGGTAGCTATGGCAGAGGGACAATTACAGGTGCTTAATGCCCTTGATGTAGCCAAAACACAATGGTACCATTTCACCGCAATCATCATCGCTGGGATGGGCTTCTTCACTGATGCATATGATCTCTTTTGCATATCACTTGTCACCAAATTACTTGGCCGCATATACTACCATATTGATGGCACAGAAAAGCCCGGAACTTTGCCTCCTAATGTATCAGCTGCTGTAAATGGAGTAGCGTTTTGCGGAACACTAGCAGGACAACTCTTCTTTGGTTGGCTTGGTGATAAGCTAGGCCGAAAGAAGGTCTATGGTATGACTCTTATGCTCATGGTCATATGCTCTATTGCATCAGGTCTCTCTTTTGGCCATACCCCTAAATCTGTCATGGCGACCCTTTGCTTCTTTCGGTTCTGGCTTGGCTTTGGCATTGGTGGTGATTATCCACTTT


gi|215516980|gb|CU602562.1|CU602562 CU602562 SEEDMAI_KZ0AAG Theobroma cacao cDNA clone KZ0AAG3YD21FM1, mRNA sequence 

TGCCAAAGGAGAGTTGCCCTG
|||||||||||| |||||| |
ACGGTTTCCTCT-AACGGGTC

EST sequence (targeted fragment marked with yellow):
TTTTTTTTTTTTTTTTGGCAATGATACTTCATAGCAAGAACAAAATGTCCAGACTAAACTTAAACACGAGATGACTAGCTCCACAAAACACAAAAGTAGGCCAATGCAGGAAAAACATCTGAATAAAAAAAATCATTTCTGGGCAATCTCCTTTGGCACTGGATTCACCGGTAACCTTTCAGAGGGTCTGCTGTTTTGCCAGACCTTGCATCAGTCCATGCTTTGGCAATTGTTCTCTTCATGTCATCATCACCGTCCTCATACATATTCTTCATTAAGTCCATGATTCCAGCCATGGGATCTCGTTCTTTATCCAAATTTGGCTTCCGCTTGTCCTCCTTGTAGTGCAGATCAGACCAGTTCCCTTTGGAAGCTTTGAACAATGTGATGACGACTCTTGTAGGCTTGACTAACGCCTTGCACTTTTCTGGTACAATGTCTTTATTCAATTTCGGAATGGCACATCGATAGTTCTTTCCTTGGACGTCATGAAATTTAACATCAAATGACATTGGCTTGAACTCTGTCTGAATTTTTTCCTGGTTAACTCCTTCTAGAGAGACATATATCTTGACTTTATCATTATCCTGATCCCAGCTGAACGAGGCGAGCGTTACATAACTCAATGCTGGGTTAACAGGAACCTTACCTGAAGTTGATATGGGAGTTGGAATTTGTGAAACAGT