Secondary structure and small RNA-seq evidence for dme-mir-979

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:19455855-19455979 +	TTAATCAC---TGGAA-----------------------CATACATGTGAG-----------GATGTCACAAATACA--------------CTGA---ATTTGGGGGGAATTCT--------TATGTATATAC-AAATTCTTCCCGAACTCAGGCTAATTTTGTG---------------GCA---------------------------TCCGTATACACAAAA----------------------------------GT------ATA
droSim1	chrX_random:5079602-5079664 +	TTAATATA---C--------------------------------------------------------------------------------------------------------------------------AAATTCTTCACGAATTCAGGCTAATTTTGTA---------------GGA---------------------------GCCGTATATACAAAA----------------------------------GT------ATA
droSec1	super_8:1738459-1738521 +	TTAATATA---C--------------------------------------------------------------------------------------------------------------------------AAAATCTTCACGAATTCAGGCTACTTTTGTA---------------GGA---------------------------ACCGTATATACAAAA----------------------------------GT------ATA
droYak2	chrX:11883259-11883281 -	TTAATGGC---TGGGA-----------------------AATAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GT------AAA
droEre2	scaffold_4690:9691773-9691867 +	TTAATCGT---TGGCA-----------------------AATACGTATGG------------GGTGCCACA------CAAATCGATTAGCTCTGA---ATTCGGGCGGAATTCTGAAGCACGCAT-----------------------------CCACTTTTGTA---------------GCA---------------------------TCC---------------------------------------------------------
droAna3	scaffold_13417:2459297-2459411 -	TAAGTTAC---TTATA-----------------------ATTAAATTTAAA-----------TATTTCGAAATAAAA--------------CTATAAAATAATTGTCTTATTTCAG------------------AAAATATGTACATATTTATACCAATCTT--------------------------------------------------------------------------------TACATATTTCAATAAAAAT------ATA
dp4	chrXL_group1e:12509670-12509797 -	TTAAGCAT---TTTAATTTTTGTATTTTTCAAGATCGAAAATATTTATGC-GCGTAAATTTAAGAGTAAGTCCTTA-GTAAGTAAGGAAG-------------------AAC------------------------------------TACGCTCTGGATTTGAT---------------ATA---------------------------CTCGTGAAGTTAAAA----------------------------------CA------ATA
droPer1	super_14:1989251-1989367 -	CTAAGTCA---TCGTG-----------------------CGCATCTGTTGG-----------GGAGTAAAAACTAAA--------------A-------TTAGAGTGGAAACTC--------TATTTTGAGTTGAATTTTTCCATGAAAATCTGCTACATTTTGG---------------G-T-----------------------------------------------------------------TTTAAATTTGTAT------TTT
droWil1	scaffold_181096:7961895-7962008 +	TAGATTATGATTAGAATAAGCACACACAACACACGCACA-----------------------------------------------------------------------CACACACACACACATCTATATAT-AAATCAACCAAGAAAACA---CAATATCGAA---------------GAAA--------------------------TTAGAAAGTATATAT----------------------------------AT------ATA
droVir3	scaffold_13042:902091-902097 -	TCAATCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6328:2896306-2896380 -	ATGAGAAA---GGG----------------------------------------------------CTATA------GAAATTGATGACG---------------------------------------------ATATAATCCAAAACTAAGATTACAATAATA---------------ATA---------------------------ATaataaac-----------------------------------------a------aaa
droGri2	scaffold_15081:2040284-2040418 -	TTGTAATT---TAAGA--------------------------------------------------------------------------------------------------------------------------TGAAGATGAAGACA----------ATAATAATAATAGTGATAGGAGTTGAAGAGCTTAAATGTAAACTGATAATTGTATATACAAAGTTGAAAATGTCATTCTCTGGTTATTGGATTAAAATGAGGACACTT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:19455855-19455979 +	TTAATCAC---TGGAA-----------------------CATACATGTGAG-----------GATGTCACAAATACA--------------CTGA---ATTTGGGGGGAATTCT--------TATGTATATAC-AAATTCTTCCCGAACTCAGGCTAATTTTGTG---------------GCA---------------------------TCCGTATACACAAAA----------------------------------GT------ATA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TTAAT-----------------------------------------------------------------------ATACAAA--TTCTTCACGAATTCAGGCTAATTTTGTAGGAGCCGTATATACAAAAGTATA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

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

Secondary Structure

dm3

-38.9	-38.7	-38.3	-38.1	-37.9

droSim1

-5.5	-5.0	-4.9	-4.6

droSec1

-3.7	-3.7	-3.5	-3.5	-3.4	-3.1

droYak2

0.0

droEre2

-19.4	-19.3	-19.0

droAna3

-6.5	-6.1	-6.0	-6.0	-6.0	-6.0

dp4

-12.9	-12.9	-12.9	-12.7	-12.7	-12.7

droPer1

-17.1	-17.0	-16.7	-16.6	-16.5	-16.4

droWil1

0.0	1.0

droVir3

No secondary structure predictions returned

droMoj3

-0.6	-0.4	-0.2	0.0	0.0	0.4

droGri2

-4.3	-4.2	-4.0	-4.0	-4.0	-3.9

Generated: 01/05/2013 at 05:34 PM