Secondary structure and small RNA-seq evidence for dme-mir-1009

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:19880562-19880652 -	CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTA---------CCCGCGATGAGTATCTCAAAA--ATTG-----TTACATTTCAGAGCGATAGCTATCCA
droSim1	chr2R:18425639-18425729 -	CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTA---------CCCGCGATGAGTATCTCAAAA--ATTG-----TTACATTTCAGAGCGATAGCTATCCA
droSec1	super_9:3164536-3164626 -	CTCTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTA---------CCCGCGATGAGTATCTCAAAA--ATTG-----TTACATTTCAGAGCGATAGCTATCCA
droYak2	chr2R:19858946-19859036 -	CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTA---------CCCGCGAGGAGTATCTCAAAA--ATTA-----TTACATTTCAGGGCGATAGTTACCCG
droEre2	scaffold_4845:21253645-21253735 -	CTGTCCATTCAAGACGTAAGTGTAAGACTTTGTTGAGTTA---------CCCACGTAGAGTATCTCAAAA--TTTG-----TTACATTTCAGAGCGATAGCTACCCA
droAna3	scaffold_13266:5750531-5750620 -	CTATCGATTCAAGATGTAAGTTTTGAATACTTCTACTCTA---------TCTTGGA-ATGTCTCTCATAA--TTGT-----CCATCTTCTAGAACGATAGCTATCCA
dp4	chr3:7562600-7562686 -	ATGTCCATACAAGATGTAAGTTCGAGAATC--------------CCAAACACATAAGTTCTTTTTTAACA------TCCAAATATTTTGTAGAGCGACAACATTCCA
droPer1	super_2:7758003-7758089 -	ATGTCCATACAAGATGTAAGTTCGAGAATC--------------CCAAAAACATAAGTTCTTTTTTAACA------TCCAAATATTTTGTAGAGCGACAACATTCCA
droWil1	scaffold_180700:5103983-5104075 +	TTATCTATCCAGGATGTAAGTATTTAAA--------GTTATTTTCAT----AATGACGGGAAATCAATGATTTGCATTC--ACTCATTGCAGAGTGATAACCTCCCA
droVir3	Unknown	-----------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6496:14788216-14788309 +	TTATCTCTACAGGAGGTAAGGACCAATTGGTA--AAGT------GAGAAATTGGAAGAAATTTATTGAAA--TTTA---TACTCGTGTTTAGGACAAGGAGTTCACA
droGri2	Unknown	-----------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:19880562-19880652 -	CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTACCCGCGATGAGTATCTCAAAAATTGTTACATTTCAGAGCGATAGCTATCCA
droSim1	chr2R:18425639-18425729 -	CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTACCCGCGATGAGTATCTCAAAAATTGTTACATTTCAGAGCGATAGCTATCCA
droSec1	super_9:3164536-3164626 -	CTCTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTACCCGCGATGAGTATCTCAAAAATTGTTACATTTCAGAGCGATAGCTATCCA
droYak2	chr2R:19858946-19859036 -	CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTACCCGCGAGGAGTATCTCAAAAATTATTACATTTCAGGGCGATAGTTACCCG
droEre2	scaffold_4845:21253645-21253735 -	CTGTCCATTCAAGACGTAAGTGTAAGACTTTGTTGAGTTACCCACGTAGAGTATCTCAAAATTTGTTACATTTCAGAGCGATAGCTACCCA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CTGTCCATTCAAGACGTAAGTGTAAGACTTTCTTGAGTTACCCGCGATGAGTATCTCAAAAATT---------------------GTTACATTTCAGAGCGATAGCTATCCA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.....................................................TCTCAAAAATT---------------------GTTACATTTCAG...............	23	1	9.00	9	9
...............GTAAGTGTAAGACTTTCTTGAGT..........................................................................	23	1	2.00	2	2
...............GTAAGTGTAAGACTTTCTTGAGTT.........................................................................	24	1	1.00	1	1
...............GTAAGTGTAAGACTTTCTTGAGTTA........................................................................	25	1	1.00	1	1

dp4

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

Secondary Structure

dm3

-11.6	-11.6	-11.3	-11.0	-11.0	-10.9

droSim1

-11.6	-11.6	-11.3	-11.0	-11.0	-10.9

droSec1

-11.6	-11.6	-11.3	-11.0	-11.0	-10.9

droYak2

-15.9	-15.9	-15.6	-15.2	-15.2	-14.9

droEre2

-11.5	-10.8

droAna3

-3.8	-3.4	-3.2	-2.8	-2.8

dp4

-1.7	-1.2	-0.9	-0.7

droPer1

-1.7	-1.2	-0.9	-0.7

droWil1

-7.7	-7.3	-6.7	-6.7

droVir3

No secondary structure predictions returned

droMoj3

-4.6	-4.5	-3.8	-3.8	-3.7	-3.6

droGri2

No secondary structure predictions returned

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