Secondary structure and small RNA-seq evidence for dme-mir-973

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:19445546-19445676 +	AATATACTTC----ACTTTA-CCGTCGTCGACTTTTCGTGGTTGGTGGTTGAACTTCGATTTTAAG-TA--TTT--------AAATAAAATGAAATCTGTTCATTCTCCGACACAAGAAGTTCACGCAAAGGA------------------------GCTGCAGCTGCGAA
droSim1	chrX:15011303-15011407 +	CG-------------------------TATACTTTTCCGGGTTGGTGGTTGAACTTCGATTTTAAG-CA--TTT--------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCACGTGAAGAA------------------------GCAGCG------AA
droSec1	super_8:1727974-1728085 +	AC------------------TTCAACGTATACTTTTCGGGGTTGGTGGTTGAACTTCGATTTTAGG-TA--TTT--------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCACGTGAAGAA------------------------GCAGCG------AG
droYak2	reseq:-1--1 *	GTTATAA--G----AT----TTTAACGTCGACTTTTCGTGGTTGGTGGCTGAACTTAGATTTTGAG-TA--TAC--------AAATAGAA-CAAATCTGTTCATTCCTCGACACAACAAGTTGACGTAAAGGA------------------------GCAGCA------AA
droEre2	scaffold_4690:9682299-9682417 +	ACTATAC--C----AT----TTTAACGTCGACTTTTCGTGGTTGGTGGCTGAACTTAGATTTTGAG-TA--TTC--------AAATAAAA-TAAATCTGTTCATTCCTCGACACAAGAAGTTGACGTGCAGGA------------------------GCGGCA------AA
droAna3	scaffold_13417:2478622-2478750 -	-----------------------GACACCGACTCCTCGTGTTTGGCGATTGAACCTGGATTTTTAA-TT--TTC--------GAGTACGA-GAAATCTGTTCATTCCTCGACACTAGTAGTTGGCGCGACA-C------TCAGCGCACCAAACATGAACCGCGGCTCAAAT
dp4	Unknown	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181096:7946449-7946592 +	AAAATATATCGGGAATATTG-TCGACATGGCCTTTTCGTGTTTGGTGATTGAACTTGGATTTTGTTCTATATACATATATAAAAAT-ATG-TAAATCTGTTCATTCCTCGACACTAGAAGTTCATGTCAATAACTTCATTT----------------CCTGCA--------
droVir3	scaffold_13042:918337-918453 -	AGAACAGTTA----AAATCATCGGACATTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTTT-TA--TAT--------A-----CA-CAAATCTGTTCATTCCTCGACACTAGAAGTTTGCGTCAATAA------------------------GCTGC---------
droMoj3	scaffold_6328:2909116-2909204 -	----------------------CGGCTTTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTAA-AA--TAT--------GAA---AA-GAAATCTGTTCATTCCTCGACACTAAGAGTTTAGG---------------------------------------------
droGri2	scaffold_15081:2051526-2051596 -	-----------------------GACATTTACTTTTTGTGTTGGGTGATTC---------------------------------------------TGATTCACTTTTCGACACATCAAGTTCACCTCAATAA------------------------ACTGCA--------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:19445546-19445676 +	AATATACTTC----ACTTTA-CCGTCGTCGACTTTTCGTGGTTGGTGGTTGAACTTCGATTTTAAG-TA--TTT--------AAATAAAATGAAATCTGTTCATTCTCCGACACAAGAAGTTCACGCAAAGGA------------------------GCTGCAGCTGCGAA
droSim1	chrX:15011303-15011407 +	CGTAT-------------------------ACTTTTCCGGGTTGGTGGTTGAACTTCGATTTTAAG-CA--TTT--------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCACGTGAAGAA------------------------GCAGCG------AA
droSec1	super_8:1727974-1728085 +	AC------------------TTCAACGTATACTTTTCGGGGTTGGTGGTTGAACTTCGATTTTAGG-TA--TTT--------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCACGTGAAGAA------------------------GCAGCG------AG
droYak2	reseq:-1--1 *	GTTATAA--G----AT----TTTAACGTCGACTTTTCGTGGTTGGTGGCTGAACTTAGATTTTGAG-TA--TAC--------AAATAGAA-CAAATCTGTTCATTCCTCGACACAACAAGTTGACGTAAAGGA------------------------GCAGCA------AA
droEre2	scaffold_4690:9682299-9682417 +	ACTATAC--C----AT----TTTAACGTCGACTTTTCGTGGTTGGTGGCTGAACTTAGATTTTGAG-TA--TTC--------AAATAAAA-TAAATCTGTTCATTCCTCGACACAAGAAGTTGACGTGCAGGA------------------------GCGGCA------AA
droAna3	scaffold_13417:2478622-2478750 -	G-----------------------ACACCGACTCCTCGTGTTTGGCGATTGAACCTGGATTTTTAA-TT--TTC--------GAGTACGA-GAAATCTGTTCATTCCTCGACACTAGTAGTTGGCGCGACA-C------TCAGCGCACCAAACATGAACCGCGGCTCAAAT
droWil1	scaffold_181096:7946449-7946592 +	AAAATATATCGGGAATATTG-TCGACATGGCCTTTTCGTGTTTGGTGATTGAACTTGGATTTTGTTCTATATACATATATAAAAAT-ATG-TAAATCTGTTCATTCCTCGACACTAGAAGTTCATGTCAATAACTTCATTT----------------CCTGC--------A
droVir3	scaffold_13042:918337-918453 -	AGAACAGTTA----AAATCATCGGACATTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTTT-TA--TAT--------A-----CA-CAAATCTGTTCATTCCTCGACACTAGAAGTTTGCGTCAATAA------------------------GCTGC---------
droMoj3	scaffold_6328:2909116-2909204 -	----------------------CGGCTTTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTAA-AA--TAT--------GAA---AA-GAAATCTGTTCATTCCTCGACACTAAGAGTTTAGG---------------------------------------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CGTATAC--------------------TTTTCCGGGTTGGTGGTTGAACTTCGATTTTAAGCATTTAAATAAGAT-AAATCTGTTCATTCTTCGACCCAAAAAGTTCACGTGAAGAAGC------AGCGAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

-----------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

-26.7	-26.7	-26.6	-26.6	-26.3	-26.3

droSim1

-20.9	-20.3	-20.1	-19.9	-19.9

droSec1

-29.3	-29.3	-28.7	-28.7	-28.5	-28.5

droYak2

-26.5	-26.5	-26.5	-26.3	-26.3	-26.3

droEre2

-30.0	-30.0	-29.8	-29.8	-29.1	-29.1

droAna3

-28.1	-27.8	-27.8	-27.4	-27.4

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

-32.8	-32.4	-32.2	-31.8

droVir3

-20.9	-20.9	-20.0	-20.0

droMoj3

-21.0	-21.0	-20.4	-20.4	-20.2	-20.2

droGri2

-15.4	-15.3	-14.8	-14.7	-14.4

Generated: 01/05/2013 at 05:33 PM