dme-mir-4977

A better ortholog for D. willistoni was not found:
- Searching the willistoni trace reads with the D. persimilis ortholog as query with LASTZ did not turn up any hits.
- This miRNA lies in the 5' UTR of the gene Eaf. The reported flybase ortholog for this gene is dwil/GK22015. Searching the entire dwil/GK22015 gene body with the persimilis sequence via LASTZ did not turn up any hits either. Apart from this, the D. willistoni ortholog reported in the mutiple alignment seems accurate given the high net which it belongs to and the high synteny of the flanking sequence.

Changes

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
droSim1	chrU	461057	G	3	0	0	0	0	0	0	0.6	0.2	0.2	5	Genomic Error	loop
droSim1	chrU	461058	A	3	0	0	0	0	0	0.2	0	0	0.8	5	Genomic Error	loop
droSim1	chrU	461059	A	3	0	0	0	0	0	0.2	0	0.8	0	5	Genomic Error	loop

Corrected Alignment

dme-mir-4977

Species	Coordinate	Alignment
dm3	chr2R:3294222-3294357 -	TTTTCGTTTAC-----TTTTTAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATACTCT------------------------------------------------------------------------GTGGCAGAAGTCT-TGC-ACCGTTCCAAAAGAG-AGCAGCACGTGGAGCGACGAGAACGGCCG-TACAATACCCAAG
droSim1	chrU:460991-461115 -	TTTT----------------TAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATACTCT------------------------------------------------------------------------GTGGCAGAAGTCT-TGC-ACCGTTCCAAAAGAG-AGCAACACGTGGAGCGACGAGCACGGCCG-TACAATACCCAAG
droSec1	super_1:944262-944397 -	TTTTCGTTTAC-----TTTTTAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATACTCT------------------------------------------------------------------------GTGGCAGAAGTCT-TGC-ACCGTTCCAAAAGAG-AGCAGCACGTGGAGCGACGAGCACGGCCG-TACAATACCCAAG
droYak2	chr2L:15977521-15977656 -	TTTTCGTTTAC-----TTGTTAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATACTCT------------------------------------------------------------------------GTGGCAGAAGTCT-TGC-ATCGTTCCAAAAGAG-AGCAGCACGTGGAGCGACGAGCACGGCCG-TAAAATACCCAAG
droEre2	scaffold_4929:19300554-19300689 +	TTTTCGTTTAC-----TTTTTAACCCTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGTGCAATACTTT------------------------------------------------------------------------GTGGCAGAAGTCT-TGC-ACCGTTCCAAAAGAG-AACAGCACGTGGAGCGACGAGCACGGCCG-TACAATACCCAAG
droAna3	scaffold_13266:3498798-3498932 -	ACCC-CTTTAT-----TTTTATTTTCACCGTT--CGAGAGGGTGTTCTCTTTGTTTTCGGCGTGCAAAACCCT------------------------------------------------------------------------TTG--AGAAGTTT-TGC-ATCGTTCGAAATTAGGGGCAGCACCTCGAACA--GTACACGGCCG-TAAAATTCCTAAA
dp4	chr3:1570003-1570137 -	TTTTTGGTT---------TTGT----------TTTGAGAACGTGCCTTCTTT-TTTTTGGCGTGCAACACTT---------------------------------TTTTC---------------------------GCGTCTCTGTGG-AAAAGTTT-TGC-ATCGTTTCAAAAAAAAAGATACACGTCGA----CACATACGGCCGCTAAGATTCCAAAA
droPer1	super_2:1744183-1744317 -	TTTTTGGTT---------TTGT----------TTTGAGAACGTGCCTTCTTT-TTTTTGGCGTGCAACACTT---------------------------------TTTTC---------------------------GCGTCTCTGTGG-AAAAGTTT-TGC-ATCGTTTCAAAAAAAAAGATACACGTCGA----CACATACGGCCGCTAAGATTCCAAAA
droWil1	Unknown	TTTTTTTTTTT-----TGTTTTACCTTTTTGT--TGAGGAAA---------------------------CATTTCAAAAAATTCTCCGTTTAAGTGCAAGAAACG-------------------------------------------------TGCTCTGCCTACG--CCAAA-----A----------------GTAATACGGCCGTAAACATTCCAAAA
droVir3	scaffold_12875:10810504-10810650 -	TTTTGATTTACTTTAATTTCGTTTGCATCGAT--T-AAAACGTGT-TTG----TTTG---CGTGCAATCACT--------------------------------TTTTCCACCGTGTC----------------CCGGC--GTGTGCGA-GAAAGTCT-TGC-AACGTACAA-------AACAACACGTTGA----TAAGCACGGCCGCAAAAATTCCCAAA
droMoj3	scaffold_6496:16132312-16132448 +	TTTT--------------------GCATCGAT--T-AAAACGTGT-TTG----TTTGCG-TTTGCAACAACT--------------------------------TTTTCCACCGTGTCCCCCA-----------CCGGCGTGTGTGCGA-AAAAGTCTTTGC-AACGTTCCAAA-------CAACACGTCGA----TAAGTACGGCCGCAAAAATTCCTAAA
droGri2	scaffold_15245:3916304-3916452 -	TTTTCGTTTG---------------CATCGATTGT-GAAACGTGT-TTG----TTTGTAGCGTGCAACACACT-------------------------------TTTT-CAC----T--CCCACCCAGCGTGTGT--GTGTGTGTGTGA-AAAAGTCTGTGC-AACGTTCAGA------AACAACACGTCGAA----CTCTACGGCCGCAAAAATTCCCAAA