dme-mir-9c

This miRNA belongs to a cluster which includes dme-mir-9c, dme-mir-306, dme-mir-79, and dme-mir-9b.
Changes
- The reported D. simulans ortholog reported in the 12-way alignment is wrong as shown below
- Two variants were flagged in from the trace data but these occur near a simple repeat in the 5' MOR region.

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
dp4	chr4_group3	8443164	T	3	0	0	0	0	0	0	0.643	0	0.357	14	Invalid - clade-specific insertion	5' MOR
dp4	chr4_group3	8443167	A	3	0	0	0	0	0	0.357	0.643	0	0	14	Invalid - clade-specific insertion	5' MOR

>dme-mir-9c
CTTGCACTATTTATCATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACATGATAT
>zdv96e12.b1:15-131
CTTGCACTATTTATCATTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA------

All strains contained the ortholog.

Corrected alignment

dme-mir-9c

Species	Coordinate	Alignment
dm3	chr2L:16697909-16698030 +	CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA------------------------------------------TGATAT----
droSim1	zdv96e12.b1:15-131 +	CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droSec1	super_7:344892-345054 +	CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAACCCA-AAACAGCCACAAATACAGGAATGATTAATGATAT----
droYak2	chr2R:4405017-4405183 -	CT----------------------------TGC-ACTA---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAGCGCACCAACCAA-AAACAGCCACAAATACAGGAATGATTAAAAATATCTTT
droEre2	scaffold_4845:19767520-19767683 +	AT----------------------------TGC-ACCT---TTTA--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCGCGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACAACGCACCAACCAAAAAACAGCCACAAATACAGGAATGATTTCTAATAT----
droAna3	scaffold_12916:15865465-15865583 -	CA----------------------------CGC-ACTCCCTTTCA--------------TTA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCACGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
dp4	chr4_group3:8443145-8443295 +	CT-CTCCCATTCGCTGTCTGTCGACTTCCATGC-ACTT---TTTGTTCTCCTT------TAA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droPer1	super_1:9894267-9894417 +	CT-CTCCCATTCGCTGTCTGCCGCCTTCCATGC-ACTT---TTTGTTCTCCTT------TAA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTAACA----------------------------------------------------
droWil1	scaffold_181061:30518-30658 -	CCTCCCCTCTTCACCATC-------------------T---TTTCCTCTCCCTCCATCATCATTTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTTTGCACATTGTATATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCA----------------------------------------------------
droVir3	scaffold_12963:12863840-12863951 -	CA----------------------------CAC-ACAA---TTT---------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTTT---ACAGTTTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCA----------------------------------------------------
droMoj3	scaffold_6500:7201331-7201445 +	AT----------------------------TGCCACTC---TT----------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTT-C--ACATATTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGACACCG-------------------------------------------------
droGri2	scaffold_14978:830199-830317 +	AT----------------------------TGC-AATT---TCTT--------------TCA-TTTTTGCTGTTTCTTTGGTATTCTAGCTGTAGATTGTTTCT---ATATCTTGTATCATCTAAAGCTTTTATACCAAAGCTCCAGCTTAAATTGCTTGCCACCGCCT----------------------------------------------