Secondary structure and small RNA-seq evidence for dme-mir-991

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:16472690-16472815 -	GTAGGATATCAAAACTATCA-------CTGCAGTTTCAGG-----CTTTTCCCAACTACACCTATTAAT----ACATATTTTA------------------ACGTCCTATTAAAGTTGTAGTTTGGAAAGTTTTGGTTTTGCATTAGAAATC-GCCACTCA
droSim1	chr2R:15134383-15134509 -	GGGGTATATCAAAAATATCA-------CTGCAGTTTCAGG-----CTTTTCCCAACTACATCTATTAAT----ATTTATTTTA------------------ACGTCGTATTAAAGTTGAAGTTTGGAAAATTTTGGTTTTGCATTTGAAATCCGCCACTCA
droSec1	super_1:14027408-14027534 -	GGGGTATATCAAAAATATCA-------GTGCAGTTTCAGT-----CTTTTCCCAACTACATCTATTAAT----ACTTATTTTA------------------ACGTCGTATTAAAGTTGAAGTTTGGAAAATTTTGGTTTTGCATTTGAAATCCGCCACTCA
droYak2	chr2R:12723766-12723891 +	GGAGGATACAAAAAAATCGC-------CTGCAGTTTCAAG-----CTTTTCCCCACTCCTTGCTTTAAT----ACTTATTTTA------------------ACGTCGTATTAAAGCCAGAGTTTGGAAAGTTTTGATTCTGCATTAGAAATC-GCCACCCA
droEre2	scaffold_4845:10619033-10619157 -	GGAGAATACCAAA-CTAGCA-------CTGCAGCTTCAAG-----CTTTTCCCCACTCCTTGCTTTAGT----ACTTATTTTA------------------ATGTCGTATTAAAGCCAGAGTTTGGAAAGTTTTGATTCTGCTTTTTAAATC-GCCACCCA
droAna3	scaffold_13266:4131534-4131677 +	TATTACTATTACAAACATTGTGCAACACTGCCGAATTGGAGACAACTTGGCTGGAATCAATCCATTCATTCTTTTCAATTTTGGCAGCCGACGGGGTAAGACCTCCCTATT-------TAAGTGGTAAAGTGATTTCTTGGAATTAAAGAA----------
dp4	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:16472690-16472815 -	GTAGGATATCAAAACTATCACTGCAGTTTCAGGCTTTTCCCAACTACACCTATTAATACATATTTTAACGTCCTATTAAAGTTGTAGTTTGGAAAGTTTTGGTTTTGCATTAGAAATC-GCCACTCA
droSim1	chr2R:15134383-15134509 -	GGGGTATATCAAAAATATCACTGCAGTTTCAGGCTTTTCCCAACTACATCTATTAATATTTATTTTAACGTCGTATTAAAGTTGAAGTTTGGAAAATTTTGGTTTTGCATTTGAAATCCGCCACTCA
droSec1	super_1:14027408-14027534 -	GGGGTATATCAAAAATATCAGTGCAGTTTCAGTCTTTTCCCAACTACATCTATTAATACTTATTTTAACGTCGTATTAAAGTTGAAGTTTGGAAAATTTTGGTTTTGCATTTGAAATCCGCCACTCA
droYak2	chr2R:12723766-12723891 +	GGAGGATACAAAAAAATCGCCTGCAGTTTCAAGCTTTTCCCCACTCCTTGCTTTAATACTTATTTTAACGTCGTATTAAAGCCAGAGTTTGGAAAGTTTTGATTCTGCATTAGAAATC-GCCACCCA
droEre2	scaffold_4845:10619033-10619157 -	GGAGAATACCAA-ACTAGCACTGCAGCTTCAAGCTTTTCCCCACTCCTTGCTTTAGTACTTATTTTAATGTCGTATTAAAGCCAGAGTTTGGAAAGTTTTGATTCTGCTTTTTAAATC-GCCACCCA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GGGGTATATCAAAAATATCACTGCAGTTTCAGGCTTTTCCCAACTACATCTATTAATATTTATTTTAACGTCGTATTAAAGTTGAAGTTTGGAAAATTTTGGTTTTGCATTTGAAATCCGCCACTCA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...........................................................................TTAAAGTTGAAGTTTGGAAAAT..............................	22	1	9.00	9	9
...........................................................................TTAAAGTTGAAGTTTGGAAA................................	20	1	8.00	8	8
...........................................................................TTAAAGTTGAAGTTTGGAAAA...............................	21	1	6.00	6	6
...........................................................................TTAAAGTTGAAGTTTGGAA.................................	19	1	1.00	1	1
..........................................................................ATTAAAGTTGAAGTTTGGAAAA...............................	22	1	1.00	1	1

dp4

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

Secondary Structure

dm3

-22.1	-22.1	-21.9	-21.3	-21.3	-21.1

droSim1

-19.5	-19.5	-19.3	-18.6	-18.6	-18.5

droSec1

-22.0	-22.0	-21.8	-21.7	-21.7	-21.5

droYak2

-32.6	-32.3	-31.6

droEre2

-30.4	-30.3	-30.1	-30.0	-29.7	-29.4

droAna3

-28.6	-28.6	-28.6	-28.6	-28.3	-28.3

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

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 01/05/2013 at 05:35 PM