dme-mir-311

This miRNA belongs to the mir-310 - 313 cluster
Note that the 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 persimilis ortholog reported in the 12-way alignment is wrong as shown below:

The persimilis ortholog is found by searching the persimilis trace data with the pseudobscura ortholog

>dme-mir-311-dp4
CATCGAGCTGCTTTGATTTGTAGGCCGTGGTTCTTGCAAATACGGATTCATAACGTATTGCACTAGCCCCGGTCCAAAAAACAATAGCAACGCCGGCAACAGCAAA
>gnl|ti|732560583:591-697
CATCGAGCTGCTTTGATTTGTAGGCCGTGGTTCTTGCAAATACGAATTCATAACGTATTGCACTAGCCCCGGTCCAAAAAACAATAGCAACGCCGGCAACAGCAAA

Corrected alignment

dme-mir-311

Species	Coordinate	Alignment
dm3	chr2R:16471367-16471480 -	TGAAAAAT--------CGA-------------------------A-----------------------------------------------AT-----------TTCTAGATCATTTTTCGGACGGTATATGGGTTAATATTT-----CAT--T-----------TGT--CGAATATATTGCACATTCACCGGCCTGAAAAT-----------------ATCAAGAATTAACAT---CG---------------------------------------AAAAG
droSim1	chr2R:15132667-15132782 -	TGAAAAAT--------CGA-------------------------A-----------------------------------------------AT-----------TTCTAGATAATTTTTCGGACGGTATATGAGTCAATATTT-----TCTTTT-----------TTT--CGAATATATTGCACATTCACCGGCCTGAAAAT-----------------ATCAAGAATTAGCAT---CG---------------------------------------AAAAA
droSec1	super_1:14025591-14025696 -	GAA-----------------------------------------------------------------------------------------AT-----------TTCTAGATAATTTTTCGGACGGTATATGAGTCAATGTTT-----TCT--T-----------TTT--CGAATATATTGCACATTCACCGGCCTGAAAAT-----------------ATCAAGAATTAGCAT---CG---------------------------------------AAAAA
droYak2	chr2R:12724807-12724923 +	TTTAAAAA--------T----------------------ATCTCA-----------------------------------------------CT-----------TTCTAGATAGTTTTGCGGACGGTATCTGCGTCAATATTT-----CCT--T-----------GTT--AGAATATATTGCACATTCACCGGCCTGAAAAT-----------------ATCAAGGACTTGCAT---CG---------------------------------------AAAAG
droEre2	scaffold_4845:10616532-10616644 -	TTGAAACC--------CCTAA------------------------------------------------------------------------------------CCCTAGATAGTTTTTCGGACGGTATCTGCGTCAATATTT-----CCT--T-----------GTT--AGAATATATTGCACATTCACCGGCCTGAAAAT-----------------ATCAAGGACTTACAT---CA---------------------------------------AAAAG
droAna3	scaffold_13266:4132915-4133034 +	AGAGAAAT--------ATT------------------------------------------------T------------------------GT-----------TGCCAGATTATCTTCAGGACGGTATTTGTGTCAATATGG-----ATA--T------------TT--CAAACATATTGCACTTATACCGGCCTGATGAT-----------------CTCCGGCGC--TCGTCATC-TG--------------------------------TGACTAAAAG
dp4	chr3:8679876-8679985 +	CATCGAGC--------T----------------------GCTTTG-----------------------------------------------A----------------------TTTGTAGGCCGTGGTTCTTGCAAATACGGAT---------------------TC--ATAACGTATTGCACTAGCCCCGGTCCAAAAAACAAT-----AGC-AACG--------C---CGGC----AA--------------------------------CAGCAAAGTA
droPer1	gnl\|ti\|732560583:591-697 +	CATCGAGC--------T----------------------GCTTTG-----------------------------------------------A----------------------TTTGTAGGCCGTGGTTCTTGCAAATACGAAT---------------------TC--ATAACGTATTGCACTAGCCCCGGTCCAAAAAACAAT-----AGC-AACG--------CCGGCAA---CA---------------------------------------GCAAA
droWil1	scaffold_180700:3453290-3453392 +	TAAT--------------------------------------------------------------------------TTATAGGCTTCGGG----GTTGTT---------------------------------GCAAAATGGTTTAT------TCTAATA-------ACTCCCCATATTGCACCTTTTCCGGCCTCTAAATTAACTTTTGA--ACAT----------------CCCGG---------------------------------------GTGGG
droVir3	scaffold_12875:13668876-13669002 -	GAAAAACT--------AGT-------------------------G-----------------------------------------------CGTC---------CGCATGACCATTTTAAGGACGGTATTTGTGACAATATGT-----GCA--GTTAAATCAATTT--GTTTAGCATATTGCACATCTCCCGGCCTAAAAAT-----------------GAACCGTGCTCTCTT---CG---------------------------------------ATATA
droMoj3	scaffold_6496:9090405-9090568 -	AAACGAAAAATGTC-------------AAATTTTCAGCTGC-------------------------------------------------------------------------GTTTGCAGGACGGTATTTGTGACAATATGAATTAT------TGAAATCAATTT--ATTCAGCATATTGCACATCTCCCGGCCTATAAAACAGT-----TGT-GAGC-----------CCGTC----GATTTAAATGATTTGTGTATTTAAAATAAATTTTCACCA-----
droGri2	scaffold_15245:17564385-17564474 +	AAAT--------------------------------------------------------------------------TTGCAG--TTCG----TGTTTAGTGTT-------------------------------------------TTTTCCC-----------GCT--TAAGCATCTTGCAAATTATATGGCTTGCAGTT-----------------ATCTGCATTAACCAT---TT---------------------------------------TCAGG