dme-mir-6-1

dme-mir-6-1

This miRNA belongs to a cluster which includes mir-309, mir-3, mir-286, mir-4, mir-5, mir-6-1, mir-6-2, and mir-6-3.
Changes
- D. simulans has a few loop substitutions which are not supported by the majority of trace reads.
- D. erecta through D. grimshawi substitutions in the miR* region are supported by the majority of trace reads.

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
droSim1	chr2R	14253986	A	3	0	0	0	0	0	0.471	0	0.529	0	17	Genomic Error	loop
droSim1	chr2R	14253990	A	3	0	0	0	0	0	0.471	0	0	0.529	17	Ambiguous - Suggested base change does not agree with neighboring species	loop
droSim1	chr2R	14253982	C	3	0	0	0	0	0	0	0.5	0	0.5	18	Genomic Error	loop

Corrected Alignment:

dme-mir-6-1

Species	Coordinate	Alignment
dm3	chr2R:15548493-15548604 -	AACTTAA-------------------------TCACAGCCTTTAATGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATATACCA--TATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CTAACATCA-TT----------------
droSim1	chr2R:14253929-14254041 -	AACTTAA-------------------------TCACAGCCTTTAAAGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATATACCA--TATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAG-GCATTTTACATCA-TT----------------
droSec1	super_1:13063224-13063336 -	AACTTAA-------------------------TCACAGCCTTTAAAGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATATACCA--TATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAG-GCATTTTACATCA-TT----------------
droYak2	chr2R:13624186-13624297 +	AGTTTAA-------------------------TCACAGCCTTTAACGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATAACAAA--TATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CTAACATCA-TT----------------
droEre2	scaffold_4845:9748744-9748855 -	AGCTAAA-------------------------TCGCAGCCTTTAAAGTAGAGGGAATAGTTGCCGTGCTGTAAGTTAATATATCA--TATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CTAACATCA-TC----------------
droAna3	scaffold_13266:9731810-9731917 +	-----------------------------------CCGCCTTTAAAGTAGAGAGAATAGTGGCTGTGCTGTAAGTTTCA-----A--AATCTATATCACAGTGGCTGTTCTTTTTGCACCTAAAGTGC--CAAACAGCC-AAACCCGAGAA------T
dp4	chr3:12677072-12677187 -	A-------------------------------CACCAGCCTTTGAAGTAGAGAGAATAGTTGCTGTGCTATATGTCCTTCGAC----TCTATATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CAAACAGCC-AAG-----GAATCGCGTT
droPer1	super_2:8906485-8906600 +	A-------------------------------CACCAGCCTTTGAAGTAGAGAGAATAGTTGCTGTGCTATATGTCCTTCGAC----TCTATATATCACAGTGGCTGTTCTTTTTGTACCTAAAGTGC--CAAACAGCC-AAG-----GAATCGCGTT
droWil1	scaffold_180701:1651298-1651414 -	T---CAA---------------------------CCAGCCTTTAAAGTAGAGAGAATAGTTGCTGTGTTTTATGCCCTTTT-C-A--ATTTCATATCACAGTGGCTGTTCTTTTTGTGCCTAAAGTGC--CCCACAACA-ACA-----ACAACAACAC
droVir3	scaffold_12875:4112589-4112722 +	GACTTAAAACTATATCGCCCAGTTATCTG--TTTATAGCCTTTAAAGTAGAGAGAATAGACGCTGTGCTGTATGTTTTGCG-TAT--GGTCTATATCACAGTGGCTGTTCTTTTTGTACCTGAAGCGC--CGTACAACG-TT----------------
droMoj3	scaffold_6496:20936294-20936412 -	TATTTATTTCTCTAG-------------TGTTTTTTCGCCTTTAAAGTAGAGAGAATAGATGCTGTG-----AGTATATCTGTTG--CATTTATATCACAGTGGCTGTTCTTTTTGTACCTAAATGGC--CAGACAGCA-TT----------------
droGri2	scaffold_5621:3389-3488 +	------------------------------------AGCCTTTAATGTAAAGAGAATAGATGCTGTGCTGTATGTTGAACG-TAT--TGTCTATATCACAGTGGCTGTTCTTTTTGTACCAAAAGTGC--CGTACAACA-AA----------------