Secondary structure and small RNA-seq evidence for dme-mir-982

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:4259824-4259946 -	TATCAAGTTAAAAAA------CGAAATCATGTTAGATCCTGGACAAATATGAAGTAAATTGTTTTTA----TGCAT--C-----------AA-TTACTTGATATT-CATCCTTG-AACTAAATG----------GTTT-TAGAGCTGCAAGA----AAAATTGT
droSim1	chrX:3274541-3274667 -	TATCAAGTTAAAAAA------CGAAATCATGCTAGATCATTAACAAGTATCATGTAAATTGAATTTTTGTATATAT--C-----------AA-TTACATGTTATT-CGTTCTTG-AACTTAATG----------GTTT-TAGAGCTGCAAGA----AAAATTGT
droSec1	super_4:2464986-2465108 +	TATGAAGTTAAAAAA------CGAAATCATGCTAGATCAAGAACAAATATCATGTAAATTGCTTTTT----TACAT--A-----------AA-ATACAGGATATT-CGTTCTTG-AGCTTAATG----------GTTA-TAGAGCTGCAAGA----AAAATTGT
droYak2	chrX:4178368-4178492 +	TATCAAGTTCAGAAA----TATAAAATCATGCTAGATCTTGGAAAAATATCTAATAGATGGTTTTTA----TACAT--C-----------AA-TCAATTGATATT-TTTCCTTG-AACTAAATG----------GGTT-TAGTGCTGCAGCA----AAAATGGT
droEre2	scaffold_4690:1630508-1630651 -	TATCAAGTTAAAAAA----TATAAAAGCAGTCCAGATCATGGAAAAATATCAAATAGATTGTTTTAT----TTCAGTCCAAACAATACATAA-TCACGCGAGTCA-TAGTATCGAAATTTAGCA----------ATTTATGAAGTTAAAAAAATATAAAGCCAT
droAna3	scaffold_13335:212413-212477 +	TTTGTGGATC--------------------------------------------------------------------------------GA-TTTCCAGTAATT-CTGCATCA-AAATCCGG-ACAAAAAATATTTT-T----------TG----AAAATTTT
dp4	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6496:5428540-5428655 -	TTG-TTGTTGGCTGTTAACAACTTGTTCGATTTGGCCTCTGGGTAGACTCTATATA-----------------TGT--A-----------AATATATAT-ATATCTAATCTCTA-ATATCTCAC----------GTTT-TACACCTGCAAAA----AAAACTTC
droGri2	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:4259824-4259946 -	TATCAAGTTAAAAAA--CGAAATCATGTTAGATCCTGGACAAATATGAAGTAAATTG----TTTTTATGCATCAATTACTTGATATTCATCCTTGAACTAAATGGTTTTAGAGCTGCAAGAAAAATTGT
droSim1	chrX:3274541-3274667 -	TATCAAGTTAAAAAA--CGAAATCATGCTAGATCATTAACAAGTATCATGTAAATTGAATTTTTGTATATATCAATTACATGTTATTCGTTCTTGAACTTAATGGTTTTAGAGCTGCAAGAAAAATTGT
droSec1	super_4:2464986-2465108 +	TATGAAGTTAAAAAA--CGAAATCATGCTAGATCAAGAACAAATATCATGTAAATTG----CTTTTTTACATAAAATACAGGATATTCGTTCTTGAGCTTAATGGTTATAGAGCTGCAAGAAAAATTGT
droYak2	chrX:4178368-4178492 +	TATCAAGTTCAGAAATATAAAATCATGCTAGATCTTGGAAAAATATCTAATAGATGG----TTTTTATACATCAATCAATTGATATTTTTCCTTGAACTAAATGGGTTTAGTGCTGCAGCAAAAATGGT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TATCAAGTTAAAAAACGAAATCATGCTAGATCATTAACAAGTATCATGTAAATTGAATTTTTGTATATATCAATTACATGTTATTCGTTCTTGAACTTAATGGTTTTAGAGCTGCAAGAAAAATTGT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...................................................................AACTACACGATATTCGTTCTTG......................................	22	1	38.00	38	38
...................................................................AACTACACGATATTCGTTCTT.......................................	21	1	1.00	1	1
...................................................................AACTACACGATATTCGTTCT........................................	20	1	1.00	1	1

dp4

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

Secondary Structure

dm3

dG=-17.4, p-value=0.009901	dG=-16.6, p-value=0.009901	dG=-16.6, p-value=0.009901	dG=-16.6, p-value=0.009901	dG=-16.5, p-value=0.009901

droSim1

dG=-14.7, p-value=0.009901	dG=-14.7, p-value=0.009901	dG=-14.7, p-value=0.009901	dG=-14.6, p-value=0.009901	dG=-14.6, p-value=0.009901

droSec1

dG=-18.2, p-value=0.009901	dG=-17.6, p-value=0.009901	dG=-17.6, p-value=0.009901	dG=-17.3, p-value=0.009901	dG=-17.2, p-value=0.009901

droYak2

dG=-18.8, p-value=0.009901	dG=-18.8, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-18.0, p-value=0.009901

droEre2

dG=-7.7, p-value=0.009901	dG=-6.9, p-value=0.009901	dG=-6.8, p-value=0.009901	dG=-6.7, p-value=0.009901	dG=-6.7, p-value=0.009901	dG=-4.1, p-value=0.009901

droAna3

dG=-1.7, p-value=0.019802	dG=-1.2, p-value=0.019802	dG=-0.7, p-value=0.009901	dG=-0.7, p-value=0.009901

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

dG=-7.4, p-value=0.009901	dG=-7.4, p-value=0.009901	dG=-6.9, p-value=0.009901	dG=-6.7, p-value=0.009901	dG=-6.7, p-value=0.009901

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 07:19 PM