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mature miRNA: TTGGCATTCTGTCCACCTCC
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|212153089|gb|CU509272.1|CU509272 CU509272 PODSSHWB2Sb_KZ0ACF Theobroma cacao cDNA clone KZ0ACF2YL10FM1, mRNA sequence 

TTGGCATTCTGTCCACCTCC
|||.|||||||| ||||.|
AACTGTAAGACACGTGGGGC

EST sequence (targeted fragment marked with yellow):
CGCGGGGTGCACAGAATGTCAATGAGCTGTTCTACGAAATAGCAAAGAGGTTGGCAAGAGCTTGCCCTCCAAAGCCATCAGGGATAAATCTAAACAATGAAAGACAGGTGAGAAGAGGGAAGCTATTTTGTTGCTTAGGTTGAAAGTCATACCATCATCTCAAGAGTCCTGGTTTAAGCTATTGATCTCAACCCTGTGGAGTACTTTTGAGCCAGACCACTCCTCCCAGAGTTGTAAGCTACTTCTTATTTCAAATGCTGGATAGCTGATTCTGAGTTTTTCTGTAAATTACTACAATAATTGTAAATAGATTGCTCAAAGGCTATCAAAAATTACTGTAATTGACTAAATACTGGAACAAGGTATACTGCTTCGAAATTTGTGATTCTTATGAAGTTCTTTCTATGCAAAAAAAAAAAAAAAA


gi|215518086|gb|CU585768.1|CU585768 CU585768 OVULEI_KZ0AAB Theobroma cacao cDNA clone KZ0AAB7YD14FM1, mRNA sequence 

TTGGCATTCTGTCCACCTCC
||||||.|||| ||| |||
AACCGTGAGACTGGTAGAGT

EST sequence (targeted fragment marked with yellow):
TTTTTTTTTTTTTTTTGGAAAGGAATAGATTTTGCTTTAACAAATCAATTAATGTGAATATTCTTAGTTGTACAAGTGCTTTGCCCGCTCTCAGACCATGAAGACTGAATTTGACAACATCGAAACCAAGGGTCACATGTCATAGGCAAAATAGCAAAGGAAATGTTCAACAGAAAAAGCCTTCACATGCTGATGAGATGGTCAGAGTGCCAATGCAAGTATCTATCCCCATTTGGATTGCTGAGCTTATAAAACAACATTATCGGTCATCCACTCCAGTTGTTGCAGGTTGCCCGGAAGATTTTTCAGCGGCCACACTTGCTTTCTGACTACCTAGCCCTGAAGAAACTTTAACCATCGCTGGTCTGACAAGTCGATCCCCAAGAAGAAATCCACGGCGAAATTCTTGGATTATAATCCCTTCCTTGAACTCTTGAGACTCCTCACGTGCTATTGCTTCATGTAGAGAGGGATCAAAGGGCTTTCCAACAGTTGGTACAACAGCCACTTGCAAACTCCTCAAGATCTCCACAAATTGCTTGTATATGCCCTGATAACTCATATCTATTTTCTTTTCCTTCTCCGTTTCTGGTTTTATTTGTTGCTTGGCTCTCTCAAAACTGTCCACCATGGGCAAA


gi|212102983|gb|CU481653.1|CU481653 CU481653 CORTEXS_KZ0AAT Theobroma cacao cDNA clone KZ0AAT3YM06FM1, mRNA sequence 

TTGGCATTCTGT-CCACCTCC
.||||||| ||| ||||||||
GACCGTAAAACACGGTGGAGG

EST sequence (targeted fragment marked with yellow):
CGGGGTCTCCAGTGGAGGTGGCACAAAATGCCAGTGAGGATGCTCGTGCTATTTGTTTGAGAGAGTATGGCAGTGCACCTGAGGTTAATATCTACGGGGATCCCAAATTTACATTCCCGTATGTTCCAACACACTTGCATCTTATGGTATTTGAGTTGGTCAAAAACTCCTTGCGTGCTGTCCGAGAGCGCTTTATGGATTCAGATAAAATTGCACCACCTGTTCGAATAATAGTTGCTGAGGGAATTGAGGATGTAACTATAAAGGTCTCAGACGAGGGGGGTGGCATACCGAGAAGTGGTCTTCCCAAAATTTTCACATACCTTTACAGCACTGCCAAAAACCCATTGGATGAATACTCAGATCTGGGAACAGCTGATACAGTAACAATGGCTGGATACGGCTACGGGCTACCTATAAGCCGCTTGTATGCTCAGTATTTTGGAGGGGATCTTCAAGTTATCTCTATGGAAGGATATGGGACTGATGCATATCTTCATTTGTCTCGTTTGGGAGATTCACAAGAACCACTGCCGTGATTCCAGTCTTGAGCACCAAAGTGGGGCAGAAGCAGGAATCATAATTAGTTCAGGGAAACATGGAACAAGGGAAATTGTGATGCATTTCTGTCAATTTTTAATCCAATAAATTGGCAGTCGTCTTGTATATTCATCATACTTTCATGTTCTACATCAGTTGGTGCAACGCAAGTAGACCCTCCTTGGTTTATAAATTGGCAGTTGTCTAAAAAAAAAAAAAAAA


gi|296178778|gb|FC072072.1|FC072072 EST00080 Theobroma cacao-Moniliophthora perniciosa pods incompatible interaction library The 

TTGGCATTCTGTCCACCTCC
||||||..|||| | ||.||
AACCGTGGGACAAGGGGGGG

EST sequence (targeted fragment marked with yellow):
TTACGGCCGGGGGGGAACAGGGTGCCAAGACTCCTGAAATATCATCTATCCTTGAAGCTTCTATAGAGAGTGATGAGTTTGTGGAGGATGCAAACCCTAAGAAGAAGCTGAAACCAAGTTCTGACAATGTTACGCCTATTGAAGACAATTCTGCAAAAAGTTTGTCTGATGAGCTATTGGCTTTGGACAATCAGATGAAGTACTTTCAAATGCCATTTATTGAGGGGAACTGGGATGCCTCAATTGATGCCTTCCTCAACGGAGATGCGACACAGGATGGTGGAAACCCAAGGGATCTTTGGAGCTTTGATGACTTCCCTGCCATGGCTGAGGGTGTTTTCTGATCAAACTTCCCCTACTTACTAGTTTTTGTAAATAAGGCAACATGAATTGGTCAATCTGTTGTGAAGTTGGAGTAAAACAGCTATACATGCGTATGCCTTGTCTGAATGTTTACAGAGGCTTTTAGTATGTTCCCTTTTGTCTATTAGACATTGAACTGCAGTGTTTAAATTTGAGTAACTGTATCTGA