dme-mir-274
Changes
The reported simulans ortholog reported in the 12-way alignment is wrong as shown below:
The correct ortholog was found in all the 7 strains trace reads using LASTZ and the melanogaster sequence as the query. The correct simulans ortholog should lie in a gap region of the assembly (chr3L:11019633-11019769).
>dme-mir-274-dm3
AGTTTTGGTGACGAATCCTGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTTGGCCGCCAGGATTACTCGTTTTTGCGATCACAAATTATGAAATTGCAGCAAAACTCAACGAAATTG
>zdo16e12.g1:275-405
AGTTTTAGTGACAAATCCTGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTTGGCCACCAGGATTACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAATGCAACAAAAATG
Corrected alignment
| Species | Coordinate | Alignment |
|---|---|---|
| dm3 | chr3L:11650003-11650132 + | AG----T---------------------------TTTGGTG-ACGAATCC-----------------TG----TGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTT---GGC---CG-C------------------------CAGGA-----TTACTCGTTTTTGCGATCACAAATTATGAAATTGCAGCAAAA-CTCAACG----------A--------AATTG |
| droSim1 | zdo16e12.g1:275-405 + | AG----T---------------------------TTTAGTG-ACAAATCC-----------------TG----TGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTT---GGC---CA-C------------------------CAGGA-----TTACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAA-TGCAACA----------A--------AAATG |
| droSec1 | super_0:3837012-3837141 + | AG----T---------------------------TTTAGTG-ACAAATCC-----------------TG----TGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTT---GAT---CA-C------------------------CAGGA-----TTACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAA-CGCAACA----------A--------ATATA |
| droYak2 | chr3L:11678621-11678750 + | TG----A---------------------------TTTTATG-CCGAATCC-----------------TG----TGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTT---GGT---CG-C------------------------CAGGA-----TTACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAA-CGCAACA----------A--------AGTCG |
| droEre2 | scaffold_4784:11632283-11632412 + | TG----A---------------------------TTTTATG-GCCAATCC-----------------TG----TGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTT---GGC---CG-C------------------------CAGGA-----TTACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAA-CGCAACG----------A--------AGTCG |
| droAna3 | scaffold_13337:5918600-5918728 + | GC----C---------------------------TTTTTTT---------------AAAAAACAGAA-A----TGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTATTTTACA---GGA---CA-----------------------TA-CAGGA-----TTACTCGTTTTTGCGATCACAAATCCTGAAATTGCAGCAAAA-AACAGCA----------A--------A---- |
| dp4 | chrXR_group6:10040179-10040309 - | CC---T----GGC----AC----------------CTGGAA-CCTGGTCC-----------------CG----TGCTGCAGTTTCATTTTGTGACCGACACTAACGGGTAATGGC-T---GGC---C-------------------------G-CAGGA-----CTACTCGTTTTTGCGATCACA-ATACTGAAATTGCAGCAACG-AGCAGCG----------A--------AACTG |
| droPer1 | super_61:320241-320372 - | ACC--T----GGC----AC----------------CTGGGA-CCTGGTCC-----------------CG----TGCTGCAGTTTCATTTTGTGACCGACACTAACGGGTAATGGC-T---GGC---C-------------------------G-CAGGA-----CTACTCGTTTTTGCGATCACA-ATACTGAAATTGCAGCAACG-AGCAGCG----------A--------AACTG |
| droWil1 | scaffold_180949:2705123-2705289 - | TT----TTGTGA---TT-ATT--------------------------------TTTAATAT------CC----TGTTGCAGTTTCATTTTGTGACCGACACTAACGGGTAGTAA---CGG---GTT--AACA--------AAGTCGTT--TTTC-TG--GCCTTTTACTCGTTTTTGCGATCACAAATTCTGAAATTGCAGCAAAAGATCAAC-GTATACAACAAACACATAAAATGA |
| droVir3 | scaffold_13049:23860698-23860839 + | AA----T---------------------------CCCAATG-TCGCATCCTGT-------------------TTGTTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTTG------GGG---CA-C---CTCGAA---------TA-CG-CTGTT-----TTACTCGTTTTTGCGATCACAAATTCTGAAATTGCAACGAAA-AGCAACA----------A-----GAAAATTT |
| droMoj3 | scaffold_6680:18485462-18485604 + | GA----ATCTGT---TG--TC------AAGTGT-------------ATCC-----------------TG----TGTTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTTGA---GG---CAT-------CTCGTA---------TT-CGC-T---GTTTTATACTCGTTTTTGCGATCACAAATTCTGAAATTGCAACGAAA-CGCAACG----------A--------AAATG |
| droGri2 | scaffold_15110:13805592-13805748 - | AAAGT-------GAA------ATAGTGCAACGTA-------TACGAGTCC-----------------TGTGCGTGTTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTTAAAG---GGC---AT-CC---TCGCA---------TTCTG-CTGGC-----TTACTCGTTTTTGCGATCACAAATTCTGAAATTGCAACGAAA-ATCAACA----------A--------AACCA |