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mature miRNA: TCACGCTGCTGTGAACATGAT
species: Medicago truncatula
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|27810960|gb|CB065382.1|CB065382 EST645063 HOGA Medicago truncatula cDNA clone HOGA-2K19, mRNA sequence 

TCACGCTGCTGTGAACATGAT
|||||||||||||||||||||
AGTGCGACGACACTTGTACTA

EST sequence (targeted fragment marked with yellow):
GGATTGTTGTTCATCAAGCTCTGGATGTCATTTTGAACAACGCAGCAACCCAAAGGATTATAGAATCATTCTTGGCAATTGGCATGATCATGGTCAAACAGAGAGGCTTGGCATAACTTGATGTGTAGTGGCACCAGAGGAGTTGTAACATTACGGACGTCAAGTCCGGGAGCTTCCTCATATACCTCAATCATGTTCACAGCAGCGTGATTTGGAAGAGGGTTGTCGAGGACATGAGGGACGTTGTTCTCAAAAGTCAACTTTCCTTGGTTAATGAGCTTCTTCACAATGTGTTTCAAAGCATAGCATCCTTCGACATCATGACCCAGAGCACCTTGATGGAAATCACATTTGAGGTCAGACCGGAACCTGGGAGGTAACGGATCAGGTGGAGGCTTCCCCTGTCTGATTGTGCAGTGCCCTCTGAGAAGTAGAGTCGGGAGCTACTCAGCATATAGCATTGGTATCAGAGGAAAGGTAGGTCTAGCCTGTTGCTACTGTCGTTGTTGGTGAACCGGTGGATGATTGTTCCTGGGCGGCTAGCAGAGCAGTCATGGTATCATTGGCCTTAGCTAATTCTTCCCTCATAGAAGCTAATTCGGTACGGAGCTGAGCATTTTCCTC


gi|55446852|gb|AJ847553.1|AJ847553 AJ847553 MtSTA Medicago truncatula cDNA clone MtTA04B07S6, mRNA sequence 

TCACGCTGCTGTGAACATGAT
|||| ||||||||||||||||
AGTGAGACGACACTTGTACTA

EST sequence (targeted fragment marked with yellow):
GCCCGGGCAGGTACTGGTCCGGGCAGCCTTATCACTCGAGGCTAAACATTCTCTTTCGAAGGCATGCTCTTAATGGGCAGATCATGAAAGACTGGCACAATCACACAGACATCGCTGACAGTCAAATAATTGTCGTTCATCAAACTCTGGATGTCATTTTGAACAACGTAGCAACCCAAAGGATTACGGAAGCATTCCGGGCAACTGGCATGATCATGGTCAAACAAAGAGGCTTGGCATAGCTTGATGTGTAGTGGCACCAGAGGAGTTGCAATGTTACGAACGTCAAGTCTGGGAGCTTCCTCATACACCTCAATCATGTTCACAGCAGAGTGATTCGGAAGAGGATTGTCGAGGACATGAGGGACGTTATTCTCAAAGGTCAATTTTCCTTGGTCTATGAGCTTTTTACAATGTACCT