>Osa04LNT0271500.1

GGATCAGAATTTACTCTCCTAGAGTTCGATTAGATTGCATATTATAAAGAGTTAGTAGTACATCAGATTTTCAGTGGGTATGCTCAGTGTGCTCTATGCGGCAATTGCCTCTCCTGGGACAAGAGATATACCGAAATTTCGATGCTTGCCATCTGCCTTGTTGATGAGCTTGAAACCTTTCAAAGGTAGCTGATTTATGAGAAGAGTTTCCAGTTGGCATGCAATGCTCTTCCCAGGTACCAAAATATATAATATCGTGGCATCCTGCATACCTTCCTTCGATCTGTGAGCACTAAGTCGACCCACAAGATCATCCGTCTGTCCAATATAGAGCTTGCTGTCACGTCTGATAATTACATAAATGCTGGACCTGCCAACAGTTGAAGGTGGGGGTTGCTCCCTAGCACCCACAGCAACACAGACCACCTCAATCAGTTCTGAGATGCTCCTTTTGTTGTAGAGATCCAACAGTTTCTTCTTGCATATTGTGGTAACAACACTCTCAATTTCTTTTCTTAGTAATCCGAAGGAACCAGATTGAAGCTCTAGTCCATTTCTCAGGTAATTAGGCTTCTCAACCAAGCTATTTACAGTAGAGTTGGCTATGGATATTTCATGGTGGACAGCTGATGATGTCTGCTTGCTGTTTGTGCTCATAGCCAAATATAGTTCCTCAGCTCTTCTAATTATCAAGTCAGGCATACCTTCTTTCCTGGCTGTTTGAAAAGCAAGACTCTCTCTACAGATGCCATCCATTAATTTCCATGTTGGCTGAATGCACCTATCGATGATTTCGGTTCCCATAGCTTTGAAATCAGTATTGTGGAGTGACAGTGGAAGGTCAAAAATGCCATGCAAATGAGTTGATATGATGCCTATGCAGCCAACATTATCGAGTCTTTCAATGATGCTACCAGCTATACATGTTCCTTTTGCTGTTTCTGTGCCCCTACATATTTCATCAATTAGAACAAGACTCCTAGCTGTAGCTCGGCAGACTAAAGATCGTATCTCTGACATTTCAATCATCAGCTGGGCTATCATATGCTTTCATATGCAGCATGATGGAATCGAAATGTGGGATGACAGCTGAAGCAGCTGGCACCATCAGGCCACATATTCCAAGTAATGCAGCAGCACAGACTGATCTCAGCATACTGGATTTACCACCACCGTTTGGACCAGTAAGAATAAACAAAGAGTGCATATGGACATCATTCAGTATTGCATTCCCTTGGTTAGTATCAAGCCAGTAAGGAAAAGTTCCTGACAATTCCATTTCACTTGAGATTTCCTCTGTAACATTATCCTTACACAAGGGAGATATAGTAGGAAGCACCCAACCCCTTCTTCGTCCTTCACTAACATGACCAAAAAGTGCTTTTGTTATGATGAGCATCGTTGAGCAAAAGACAAGGACATTAATCTTGTCCTGCAATTCACTTGAAAGTCCTCTCAACAACTCAAGAACTTTACGTTTTGCATTATCACAAGCTTCATGGTACCTGGTTAAAGCATTCTCAACTTTGATAGTGGTGAACCATTCTTCTCCGACCTTTCTACCTTTTGAGTCAATTGCAGGCTTCAATTGCTTTATCTGTAGTTCACCAGGAGTGTTGGCCCACACATTTGGTGTGAATCGCCTCCCTTTAAACCAAACAGATTCATGCTCTTTTGCATAACTGATTTCTCCCTTCGAACTTCCATTTGAGGACATCACAGATTTTACTCTTGAAATAATTGGCAGAAAATCTTCAATGACCGCTGTTGACAGTGCCTCAGCAGCTATATCAACATTTGAGAACTCCTCTTCAGCATGCACCCTTTTTACACGTCCCTTCCAAGATGACTCCATATCATTGAAGAACTCTTTCGGAATATATTCAGATGAAGTTATTGCCTGGTCACTTTCACCACCTAAAGAGATTACTTCAGCTATACGTTGTGAAATAAAGCTACATTCATTCACTAGTATATCGGCTTCAACTTTGAACCCAGTAACTATGGCGGCAGGATCAAGCAATTTATTCAGGATAGCAGAAAGCTCAGCATTGCTACCCATGAACAACACCTCATCGAGGACATTCTTTATTCTACAAAATTCGATGTGATTAACCTCTTTTGACTCGAGTAATTTCACAAGCTTTGCTGCCGGTATGCATGTAAATTCAGGAATCGAGCAAGTTATGCTACCCATAAGCCTGCAAGCCTCTTGAACTGATGATGCAACATCAAAAGATGGAGGGTTAAGAAGAAGATCTCTAATATACAATGATGGAAGGCCACCAAAGTTTGGAGGGAGAACAATTTTTAGCAAACTGGGTATTCCCTCAGTTGGTATCACCCCAATTTGAGTAGCTGTTCCAAGATACAAGGGTTGAGGCCTCCCTTCCAATGAGACACTGACATTACGGAAAACAGTCTTCTCTTCAAGCCCATATATTTCCCTTACCTTGCATAACAGTTCTTCAATAGGATTACCATCAAACCACTCAAAAGATTTTCCACTGCACTCTCCCCACAATAGCCCACCTTCGCCAAATTCTCCCCAGCGTGATGTGCCTGAAGAATTGTTCCTCAAAGAACTATGAAGGTATAGATGATGATAACGGCATATGCGAAGCTTAGTAACAACTGCTTCCTCTGTTAAGCCCTCCTCAGCTGAATATGTTTTCATTGTCTCTAGCACAGAAATCAGGCAATAGCCTTTTGCAGATCGTGAAATCCCAACTACAGGCATTGGATCAGGGAACTCAACATCATGGTCTACTTCAGCAAGACCAAATACATAAGGACTACCAGGATGTGCATGGCCAGAAATAAATCGGCCTTTCCTAGCACGAGCTTGGGTTGGGCCTTGAATTTCTTCAACTATGCACACAGAGTAACCACATCGAGTCAAATCATCCAATGTCTGCCGCAAATTCATGACTGGACATCCAGCTTTTGGAATACTATCAGAACGCAAGCCTCCAAAAGGATTTAAGCCTGCATGCTCCACAAGGATACATGCATCAAACCCAACAGCCTCGTAGAAATCTCCCACTCTGCAAAGTAGAACTTCACGAGGAAACTTCGATTTGAATTGCAACATTTCCGTGTTCAGGCTTCCATCCTTCAAGCTTCCATTTCTTAAAGTTGGATCCAATCCTAAAATATTTGAATACACAAGTCTCTGAGTCAATTGCATTGATGATGGTTTCCTGCACCTCTCCATTTTC

Explanation	CPC Score
noncoding (weak)	-0.956857

Transcript ID	Chromosome	Locus	Ref	Alt
Osa04LNT0271500.1	4	25325435	T	A
Osa04LNT0271500.1	4	25326349	G	A
Osa04LNT0271500.1	4	25327431	C	A
Osa04LNT0271500.1	4	25327528	A	G
Osa04LNT0271500.1	4	25327955	A	G
Osa04LNT0271500.1	4	25324707	T	C
Osa04LNT0271500.1	4	25326132	C	T
Osa04LNT0271500.1	4	25328963	G	C
Osa04LNT0271500.1	4	25329401	A	G
Osa04LNT0271500.1	4	25329601	C	T
Osa04LNT0271500.1	4	25331432	G	A
Osa04LNT0271500.1	4	25331673	T	G
Osa04LNT0271500.1	4	25331907	G	A
Osa04LNT0271500.1	4	25336660	A	G
Osa04LNT0271500.1	4	25337125	A	T
Osa04LNT0271500.1	4	25334370	A	C
Osa04LNT0271500.1	4	25334475	C	T
Osa04LNT0271500.1	4	25334649	T	C
Osa04LNT0271500.1	4	25335362	G	T
Osa04LNT0271500.1	4	25331991	A	G
Osa04LNT0271500.1	4	25332286	T	G
Osa04LNT0271500.1	4	25332697	G	A
Osa04LNT0271500.1	4	25335725	A	T

Transcript ID	Transposon ID	Chromosome	Strand	Start	End	Counts
Osa04LNT0271500.1	DTM_#DNAt_MULE_japo_Os0709	Chr4	-	25334291	25335523	1232

Transcript ID	MiRNA ID	Inhibition	Expectation	Score	Binding Start	Binding End
Osa04LNT0271500.1	osa-miR5542	Cleavage	4.5	9.518	1	21
Osa04LNT0271500.1	osa-miR5817	Translation	4.0	10.563	1	24
Osa04LNT0271500.1	osa-miR1440b	Cleavage	4.0	10.586	1	21
Osa04LNT0271500.1	osa-miR6246	Translation	4.0	15.513	1	23
Osa04LNT0271500.1	osa-miR159a.1	Cleavage	5.0	15.761	1	21
Osa04LNT0271500.1	osa-miR159b	Cleavage	5.0	15.761	1	21
Osa04LNT0271500.1	osa-miR1866-3p	Translation	5.0	18.211	1	22
Osa04LNT0271500.1	osa-miR1879	Cleavage	5.0	15.695	1	24
Osa04LNT0271500.1	osa-miR2864.2	Translation	4.0	11.974	1	21
Osa04LNT0271500.1	osa-miR5156	Translation	4.5	13.001	1	24
Osa04LNT0271500.1	osa-miR5161	Cleavage	5.0	14.615	1	20
Osa04LNT0271500.1	osa-miR5505	Cleavage	5.0	12.879	1	22
Osa04LNT0271500.1	osa-miR5508	Cleavage	4.0	14.588	1	21

Transcript ID	Chr	QTL Gene	Character Major	Character Minor	Marker Interval1	Marker Interval2
Osa04LNT0271500.1	4	qChla4-1	Morphological trait	Shoot/Seedling	C2807	RM241
Osa04LNT0271500.1	4	qChlab4-1	Morphological trait	Shoot/Seedling	C2807	RM241
Osa04LNT0271500.1	4	pss4.1	Physiological trait	Source activity	RZ740	RZ590
Osa04LNT0271500.1	4	qPH1-4-1	Morphological trait	Dwarf	RM241	C2807
Osa04LNT0271500.1	4	nan	Resistance or Tolerance	Other soil stress tolerance	RM5586	RM3916
Osa04LNT0271500.1	4	gpp4	Morphological trait	Seed	RZ569	RZ565
Osa04LNT0271500.1	4	nan	Morphological trait	Culm/leaf	RM3785	RM1388
Osa04LNT0271500.1	4	nan	Morphological trait	Culm/leaf	RM3785	RM1388
Osa04LNT0271500.1	4	nan	Morphological trait	Culm/leaf	RM3785	RM1388

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

Transcript ID	Chromosome	Locus	Trait	Value	Plus Minus