>Osa02LNT0176000.1

ATCAAATCAATCACAATTTTTTTCATACGGAAACATTTTCAGAGTCTACATTCACAAGTTCAGAACTCGTAACAAAAAAGAGAAAGCAGAATTACATTTTGTATTTACAAAGACACCACAAAGAACTCCTCACAGTATTAACTGTAAGTCTGATGTTTGACTGAACCTACAGAATTGTGTATTACAAATCTACAGTAAGCAAAATGTTGGATCTTTTTAAAGTATTTATAGTGATAAAAAAGTTGACTAATGGACCTACCTTTACAAGCACATCAGAATAATACAGTCAAGAACACCAACTCTTGCAGAAGTTTATGTTGGAGTTGGAGCAGCAGCTGCCCTCATGAGCATGAATCTCCTCCTCGCAATATTGTTTGCATTTTCACCTAGCGCAGCCAGGTGAAGCATCCGCCGCCTTGCTGCCGCCACAGCAACATCATCTGCGGTTGGCTTCCCAGGAACCTCATGAGGTGGTGAGCTCTCCCCTGATGCCTCGACGTCACCATCCAATTCGTTGTGCTGCATCACTTGCTTTATGCTCTCCACCACCTCTCTCATAGTTGGGCGGTCTTTTGCATGTTTTGCAAGGCAGCTGTTGGCCAATTTGGCAATTTCTCTAGTGCCCTGCTTAGAGTAATTGTGCCTGAGTCTGATATCTATAATCCTGCTGAACCTCTTAGTCTCAACAGGATACTGCCTCACCCATTCCAGGAGTTTCTGCTCGTTCTTGGGACGATTCCTTTCCATTGAACGGCGTCCGGTGAGGATCTCATATAGGACAACTCCAAAGCTCCAAACATCACTCTTGTTTGTGAGATGGCCTGTCTCAACATAGTCTGGAGCTGCATAACCATAAGTCCCCATAACCGCTGTGGACACATGAGTGTTATCTGCAGTTGGCCCTTCCCTTGCTAATCCGAAGTCTGAAAGTTTCGGTCTGAATTCCTCATCAAGTAGCACATTGGATGCTTTGAAATCACGGTATATGACCTATAAAATTTTCAAGTCTGAAACAAGAATTTTCTGTGTTTCCTCAAGCAAAGTCAAAACCATAATTGACAGGATTGCATTTTTAAGGATCTCTTAAAAGCCATTTACAAGCTGGAGGTAACATTCATCGTTGGGAGAATAGCCACTATGGTCCCTGAAGTTTCGCTCTGAGATCATTTTAGTCCCTGACCTTTCAAATTGTCCAAGCAAGCCCTTAAACTTTATCATGTGGACATATACAGTCCTTGGCCCATCGAAAATTGCCACGTGGACATGCCATGTCATCTTCCAATGCAAATATATGATGACATACCCAATTTTCCCTTACACATATCGTCATAGGGAAAAAAGAGAGAAAGAAAAGGAGAAAAATAATAATAATAAAGAAGTAGGTGATCCTGCATATTAAATATCCGTTAGAGTTTTAACATTGAAATGCAACTACTTACATGAAATTTATTTGGCATGATAATTATATATTTAGTGGTTGTAGCTAATTTAACTTTGTATTAGCATAATCCAGTGAAAAAAGTTTGCCATATATCCAGTCACATTGAATAAAGTTTGTAAATTCTTTTCATTATTTTTTATGGTACATGGAAGGGTAAATTGGACATTTTACCATATATTTTGCATGAGAGCATAACATGGCATGCTCATGTGGCAATTTAAGTGGAACTAAGGACTATATTAGCCCACATGACAAATTATAAGGACTCGTTTGGACAATATAAAAGGTTAGGGACCAAATTAATCATGGAGCAAAACTTCAAGGATCATGTTGGCTATTCTCCCTTCATCGTTCATGGTAATCATTTTCTTTCAAGTATGTCCCATTCAATCAATATGTCATATGACTCAACGGACATTCAAAATACTTGCAATAAAAAGGATTGAGTAATATGTCCATCCAAGCTATATGATTAGATTCATTCCAGATCTCCAGTCATGAAATATATAGTTAACTTTAAAATTCAGAAGTGTTGCAAAAAGATCAACATAATTGACTTGCAGACAACCATTCTTGCACAGCATTTGCTAAATCACAACATTAATATGGTATGGCTCAGGGACACCAACAAACTGTGAGGCCTTTAGCAATATAACTCTATTAAAAGCTGTCCTATTTCAGACTTTAGGGGAGAAAATGGGTAATCCGTTATGATTCAGATGAATAAAATGAATTTCTTGATGGTGAGTTGCCAGCGGTGTTACCTGAACTTCCAATCCCTCATGGAGGTACAACAACCCCTCAGCAGCACCCAATGCTATCTTCAACCTGATGTCCCATGGGAGGACGGGATATGCTTTATTGAATAGATGATCATCCAAGGTCTTGTTCGACATGAACTCATATACCAGCAACCTCTGAGGGCCTCGTTCACTCTGAGCGGCACAATATCCAATGAGCTTGACGAGATTCGGGTGCTCAACAACCCCTAGAAATTGAACTTCTGTCAGCCATTGCTTGTGACCCTGTCGGCTGTTGGGATTGAGCTTTTTTATGGCGACCTCGGTGCCACCGGCGGGCCCTCCGGGCAGCCGAACGACGCCCTTGTAGACGCTCCCGAAGCCGCCCTCGCCGATCTTGAGCAGGCGGCTGAAGTCCCTGGTCGCCGCCTGGAGCTCCCGGAGCCCGAACTCCTGCAGGGAGCTCGCGCCCCTCTCCTCGTACAGCTCCGGGATGCTCCGCGCCGACGAGACCGACCCGGACGACCTGCTCCACCCGGCGGCGGGCCTCGCCGCCGCCGCGCTCGAGTCCTCGGTCGACTGGCTCGTCGCGACGGCCGACGACGACACCGTGGAGGTGGAGTGGGACGAGCCGGCGAGCGCCGACGGCGGCGGCGGCGGCGGCGCTGGCCCCTCGTGCGGCGGCGGCCTCTTCTTCCCCTTCCGCTTCTTGATCATATCCCTCACGCGGCCGAAGCAGCCCATCTCCGAGGAACAGTAAGCTGGAGAGAGGGGGATTCGGGTCAGCTCGTGGTGCTCTTCTCCATGGCCTTCACCTCGTCAGCTCGAATCGTGAGGAGAAAGGGAGCAACCTTTCGGCGATAGAAACGGAAGCCTTCTTCTTCTTCCTTCTCCTTGCTGATCGGATACAACTACAAGAACTATTTTCTCCTGGCCTCCACGAAACACGACAACAAACGGAGACGAACACGAACGAACTCGCGTGAGTCGGTAAACTGACGCAGAATCGTTTGACGCAAGCAAGGACGAGGGAAGGATGACACCAATTTGTGCTGGGTGAACAGGAAGTTCGAGTGTATTTTCCTTGTTCTTTTTCCCCTGGGAGGCGAAGAATTTTGAGCCACGC

Explanation	CPC Score
noncoding (weak)	-0.625828

Transcript ID	Chromosome	Locus	Ref	Alt
Osa02LNT0176000.1	2	26209442	T	C
Osa02LNT0176000.1	2	26212505	A	G
Osa02LNT0176000.1	2	26210044	A	G
Osa02LNT0176000.1	2	26210077	G	A
Osa02LNT0176000.1	2	26211195	T	C

Transcript ID	Transposon ID	Chromosome	Strand	Start	End	Counts
Osa02LNT0176000.1	DTM_#DNAt_MULE_japo_Os0301	Chr2	-	26210248	26210910	662

Transcript ID	MiRNA ID	Inhibition	Expectation	Score	Binding Start	Binding End
Osa02LNT0176000.1	osa-miR5179	Cleavage	5.0	14.973	1	21
Osa02LNT0176000.1	osa-miR7692-3p	Cleavage	3.5	17.982	1	24
Osa02LNT0176000.1	osa-miR160f-3p	Translation	4.5	19.104	1	21
Osa02LNT0176000.1	osa-miR1428e-3p	Translation	4.5	9.707	1	21
Osa02LNT0176000.1	osa-miR396f-3p	Translation	4.5	17.663	1	24
Osa02LNT0176000.1	osa-miR2873b	Translation	5.0	14.293	1	21
Osa02LNT0176000.1	osa-miR5152-5p	Translation	5.0	11.798	1	21
Osa02LNT0176000.1	osa-miR5157a-5p	Translation	3.5	8.599	1	24
Osa02LNT0176000.1	osa-miR5157b-5p	Translation	3.5	8.599	1	24
Osa02LNT0176000.1	osa-miR5524	Translation	5.0	14.077	1	21

Transcript ID	Chr	QTL Gene	Character Major	Character Minor	Marker Interval1	Marker Interval2
Osa02LNT0176000.1	2	qPH-2	Morphological trait	Dwarf	RG324	RG83
Osa02LNT0176000.1	2	yld2.1	Morphological trait	Seed	RM262	RM263
Osa02LNT0176000.1	2	qSS-2	Physiological trait	Sterility	RM301	RM263
Osa02LNT0176000.1	2	qSB-2	Resistance or Tolerance	Sheath blight resistance	G45	RZ273
Osa02LNT0176000.1	2	nan	Physiological trait	Eating quality	C621	C370
Osa02LNT0176000.1	2	Hbd2	Physiological trait	Lethality	nan	nan
Osa02LNT0176000.1	2	qCSH2	Resistance or Tolerance	Cold tolerance	RM262	RM263
Osa02LNT0176000.1	2	nan	Others	Others	C424	G45
Osa02LNT0176000.1	2	Sn2a	Morphological trait	Dwarf	C424	G45
Osa02LNT0176000.1	2	Tiller number	Morphological trait	Culm/leaf	R26	C424
Osa02LNT0176000.1	2	qRPA-2-c	Resistance or Tolerance	Other soil stress tolerance	C424	G45
Osa02LNT0176000.1	2	qGRH-2	Resistance or Tolerance	Insect resistance	C621	C601
Osa02LNT0176000.1	2	qPTD-2	Morphological trait	Panicle/flower	C424	G45

Transcript ID	Pre-miRNA	Identity(%)	Alignment Length	Pre-miRNA start	Pre-miRNA end	E-value	Bitscore

Transcript ID	Chromosome	Locus	Trait	Value	Plus Minus