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mature miRNA: CACTACATTATGGAACGGAAG
species: Hordeum vulgare
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|161446594|gb|EX572464.1|EX572464 HDP31P08T HDP Hordeum vulgare subsp. vulgare cDNA clone HDP31P08, mRNA sequence 

CACTACATTATGGAACGGAAG
 |||||||||||| ||||| |
ATGATGTAATACCCTGCCTCC

EST sequence (targeted fragment marked with yellow):
AAAAAAATACTCTTAAATTATGGGATGAAAGGACTAATGCACAAAGTATAGTGCATCTATCAAAACAAATACAATGTACTCCCTCCGTCCCATAATGTAGTAGTGTCAAAAACCGTACTACATTATGGAGGGAGTATGACTCTGTCTGTATACAGGGAAGCCAAAAGCAAAACAGGCACATTTTTATTCGGCACCCAGCGAAAGAAACTGGTCAGAAGAACAATTACAACAAAAAATGAAACAAACCAGAGTGCTTTGGTCGCTGTTTAAAACTCGACGCGACATTAGTTACAGAAAAGTTGAACCAAACCTATTAGTTATAATTAACTAGCCGTAGTATAGTACGTCGCTCATTCCTTCTACAATCAAGGGAGAGGGTACTGAGATGAAGAAGAAGAATATTTCGAAATGCAATTAACGAATTTGATGGAGAGACTGCTGATGGAGGCCTACGCGCGTCGCCGGTGCGGGGGACGGGACGACAGCTCGTAATTACGTACGTGGTGCAGTATACTGACGCGCTCACGCGCACTGCTTCTACTCGGGGTTGG


gi|60274121|gb|DN178864.1|DN178864 HO31K20S HO Hordeum vulgare cDNA clone HO31K20 5-PRIME, mRNA sequence 

CACTACATTATGGAACGGAAG
| ||||||||||||||| |||
GCGATGTAATACCTTGCGTTC

EST sequence (targeted fragment marked with yellow):
GCACGAGGCGAGAAGGGGTCTAACTGCTGCACCGAGTGCAGGAAAGGGGGCGGCGTCAGGGATTACTGGTTCTACCGCTCCACCTGCAAGACCGTGTACCTGCATGTCAGCTGCGCGAAAGAGGGTTTTCTTACGCCGGGCTCAAGTAGTACCGAGCCCGACGTCGACGATCATGGCAGCCTGGCCCGTTTCGTCAACGACACTGCGTCGCGGAAGCACAAGCACGGGCCAGGGAAGTCCGGGCAGAACTGGGAAATAATAGTCGACATCATTAAGGCCCTGACGGGCATCATCATCGCGGTGCTCACTGGAAATCCGGCGCCGTTAATTCTTGCAGGTTTCGATCTGGGCTCCAACGTCATCAAATCCTTGAGAACCAGGTAGCTAGCTAGCAGCTTCATCCAGCTTGCTCATCCTCATCGTTCTACGGGTTGCATAATGACATATATTCTACTTCTTGCGTTCCATAATGTAGCGTGTCCGTGTTTTCCAAATTTAAATTTAATTATAAATTTAAC


gi|60275174|gb|DN179917.1|DN179917 HO28L20S HO Hordeum vulgare cDNA clone HO28L20 5-PRIME, mRNA sequence 

CACTACATTATGGAACGGAAG
|||||||||||||||||||||
GTGATGTAATACCTTGCCTTC

EST sequence (targeted fragment marked with yellow):
GCACGAGGCTCACGTTCGAGCTCCGCACGCAGGTGTCTCACTGCTGCACCAAGTGCAGAAAAGGTGGCGGCGTCAGGGATTTCTGGTTCTACCGCTCCACCTGCAAGACCGTGTACCTGCATGTCCGCTGCGTGATAGAGGATTTTCTTACGCCGAGCTCAAGTTCAAGCACCGACGGTAATAGCAGCCTGGCCTGTTACGTCAAGGAGACAACGTTGCAGAAGCACAGGTCAGGGAAGGCCGAGAGGAACTTCGACCCCATATTCGAGATCGTTAAGGCCCTGGCCAGCATAATCATAGCGGTGCTCACAGGAAATCCGGCGCCGGCAATTCTTGCAGCTTTCGATCTGGGCTCCAACGTCATCAAATCCTTGAGAACCAGGTAGCTAGCTAGCAGCTTCATCCTGCTTGCTCATCCTCATCGTTCTACGGGTTGCATGATGATATATATTCTACTTCTTCCGTTCCATAATGTAGTGTGTCCGTGTTTTTCAAAATTTAAATTTAATTATAAATTTAACCAACGAGAACAATTGCGGAGGGTTTAAAATTATATCATTGAATTCATATTCAAAAAAAGGTTTTGAAGGGTATAATTTTTGCTCCCGTCGCAACCATCAACGTTGGTTAATTTATGAATAAAAT