dme-mir-311

This miRNA belongs to the dme-mir-310 - 313 cluster
Note that the D. grimshawi ortholog is confident in the alignment even though it has discordant substitution patterns and it does not fold into a hairpin structure:

Changes

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
droGri2	scaffold_15245	17564435	T	3	0	0	0	0	0	0.714	0	0	0.286	14	Genomic Error	miR
droSim1	chr2R	15132728	A	3	0	0	0	0	0	0.4	0	0.6	0	15	Genomic Error	loop
droSim1	chr2R	15132760	G	3	0	0	0	0	0	0	0	0.357	0.643	14	Genomic Error	3' flanking region

The reported D. persimilis ortholog reported in the 12-way alignment is wrong as shown below:

The D. persimilis ortholog is found by searching the persimilis trace data with the D. pseudoobscura ortholog

>dps-mir-311
CATCGAGCTGCTTTGATTTGTAGGCCGTGGTTCTTGCAAATACGGATTCATAACGTATTGCACTAGCCCCGGTCCAAAAAACAATAGCAACGCCGGCAACAGCAAA
>gnl|ti|732560583:591-697
CATCGAGCTGCTTTGATTTGTAGGCCGTGGTTCTTGCAAATACGAATTCATAACGTATTGCACTAGCCCCGGTCCAAAAAACAATAGCAACGCCGGCAACAGCAAA

Corrected alignment

dme-mir-311

Species	Coordinate	Alignment
dm3	chr2R:16471367-16471480 -	TGAAAA-----------------A-TCG---AAATTTCTAGATCATTTTTCGGA--CGGTATATGGGTTAATATTTCAT------------TTGTCGAATATATTGCACATTCACCGGCCTGAAAATATCA-A--GAATT-------AACATC-----------------------------------GAA---AAG
droSim1	chr2R:15132667-15132782 -	TGAAAA-----------------A-TCG---AAATTTCTAGATAATTTTTCGGA--CGGTATATGAGTCAATATTTTCT----------TTTTTTCGAATATATTGCACATTCACCGGCCTGAAAATATCA-A--GAATT-------AGCATC-----------------------------------GAA---AAA
droSec1	super_1:14025591-14025696 -	GAAA------------------------------TTTCTAGATAATTTTTCGGA--CGGTATATGAGTCAATGTTTTCT------------TTTTCGAATATATTGCACATTCACCGGCCTGAAAATATCA-A--GAATT-------AGCATC-----------------------------------GAA---AAA
droYak2	chr2R:12724807-12724923 +	TTTAAA-----------------AA-TATCTCACTTTCTAGATAGTTTTGCGGA--CGGTATCTGCGTCAATATTTCCT------------TGTTAGAATATATTGCACATTCACCGGCCTGAAAATATCA-A--GGACT-------TGCATC-----------------------------------GAA---AAG
droEre2	scaffold_4845:10616532-10616644 -	TTGAAA-----------------C-CCC---TA-ACCCTAGATAGTTTTTCGGA--CGGTATCTGCGTCAATATTTCCT------------TGTTAGAATATATTGCACATTCACCGGCCTGAAAATATCA-A--GGACT-------TACATC-----------------------------------AAA---AAG
droAna3	scaffold_13266:4132915-4133034 +	AGAGAA-----------------A-TAT---TTGTTGCCAGATTATCTTCAGGA--CGGTATTTGTGTCAATATGGATA-------------TTTCAAACATATTGCACTTATACCGGCCTGATGATCTCC-G--GCGCTCGTCATCTGTGAC-----------------------------------TAA---AAG
dp4	chr3:8679876-8679985 +	CATCGA-----------------GC-TGCTTTGATTTGTA-----------GGC--CGTGGTTCTTGCAAATACGGATT---------------CATAACGTATTGCACTAGCCCCGGTCCAAAAAACAAT-A--GCAA-CGCC---GGCAAC-----------------------------------AGCAAAGTA
droPer1	gnl\|ti\|732560583:591-697 +	CATCGA-----------------GC-TGCTTTGATTTGTA-----------GGC--CGTGGTTCTTGCAAATACGAATT---------------CATAACGTATTGCACTAGCCCCGGTCCAAAAAACAAT-A--GCAA-CGCC---GGCAAC-----------------------------------AGC---AAA
droWil1	scaffold_180700:3453290-3453392 +	TAAT-------------------------------TTATA-----------GGCTTCGGGGT-TGTTGCAAAATGGTTTATTCT-----AATAACTCCCCATATTGCACCTTTTCCGGCCTCTAAATTAACTTTTG-----------AACATCCCG--------------------------------GGT---GGG
droVir3	scaffold_12875:13668876-13669002 -	GAAAAA-----------------C-TAG-TGCGTCCGCATGACCATTTTAAGGA--CGGTATTTGTGACAATATGTGCAG-TTAAATCAATTTGTTTAGCATATTGCACATCTCCCGGCCTAAAAATGAAC-C--GTGCT-------CTCTTC-----------------------------------GAT---ATA
droMoj3	scaffold_6496:9090405-9090568 -	AAACGAAAAATGTCAAATTTTCAGC-TG---------------CGTTTGCAGGA--CGGTATTTGTGACAATATGAATTATTGAAATCAATTTATTCAGCATATTGCACATCTCCCGGCCTATAAAACAGT-T--GTGA-GCCC---GTCGAT---TTAAATGATTTGTGTATTTAAAATAAATTTTCACC-----A
droGri2	scaffold_15245:17564385-17564474 +	AAAT-------------------------------TTGCAGTTCGTGTTTAG------T-----------GTTTTTTCC------------CGCTTAAGCATCTTGCAAATTATATGGCTTGCAGTTATCT-G--CATTA-------ACCATT-----------------------------------TTC---AGG