Secondary structure and small RNA-seq evidence for dme-mir-955

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:3299040-3299166 +	TAAGGAACACTTTTTGGCC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTTTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA--ACAA-------------------------------------------------TT
droSim1	chr3L:2834561-2834687 +	TAAAGAACACTTTTTGGCC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTTTTGCCTAATCGCATTCAATTTCTGCACGGTAGAGATGGTACGCTTAGAAACAACCTAAA--AAAA-------------------------------------------------TT
droSec1	super_2:3291343-3291466 +	TAATAAACACTTTTTGGTC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTTTTGCCTAATCGCATTCAATTTCTGCAG---AGAGATGGTACGCTTAGAAACAACCTACA--AAAA-------------------------------------------------TT
droYak2	chr3L:3844747-3844864 +	TAAAGTAAA---------C--AGCTAATCAACTCCATCGTGCAGAAGTTTGAGTGTCCTGT---GTGTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA--ATGA-------------------------------------------------GT
droEre2	scaffold_4784:5981989-5982116 +	AAGGAATACACTTTTGTCC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGT---GTGTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA--GCAA-------------------------------------------------GT
droAna3	scaffold_13337:7606422-7606539 +	TGAAGGATGTTTTTTGAGA--AGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCTAAT----TTTTAACCATTCGCATTCAACCTTTGGACGGTAGAGATGGTCAGTGAGAAAGCAACCTA-----------------------------------------------------------
dp4	chr4_group1:2379981-2380081 +	AATT----------TAAAA--AAATGAATAAATTCAAATGACAAAAATGTAAATGAATTAA-----------AAAATAAATTCAAATGATAAAAAGTAAA----------TGAATAAAAAAATAAAGTAAAA-------------------------------------------------TT
droPer1	Unknown	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_180698:10215726-10215851 +	ATTCAAATACTTTTGCGTTAAGGTTGGCTGGCTCCATCGTGCTTAGGTTTGAGTGTCTTCGTTTGTTTTCTCTAATGGCATTCAACCTTGGAGCGATAGAGACGGCCAATCGAGAAACAGCCTAAA---------------------------------------------------------
droVir3	scaffold_12758:855562-855687 -	TATGTATGGATCTCTCATC--AGTTAGCTAGCTCCATCGTGCACAGGTTTGAGTGTT-TGA---GTTTTTCCTAGTGGCATTCAACCTTTGAACGGTAGAGATGGCCAACTGAAAAGCGACCTAAA--CTAA-------------------------------------------------TA
droMoj3	scaffold_6680:1909563-1909732 -	TCAGGTATCCAATATG-----GGTTAGCGAGCTCCATCGTGCACAGGTTTGAGTGTT-TGT---GT-TTGGCTAGTCGCATTCAGCCTTTGAACGGTAGAGATGGCCAACTGAAAAGCGACCTAAC---TGAAAGCGAATCAAGGGAACTAGGCCAATAGGCGAGAATCATATAGAAATAGTT
droGri2	scaffold_15110:657067-657177 +	TAAAG-----------------GTTGGCGAACTCCATCGTGCACGGGTTTGAGTGTC-TGA---GT-TTGCCAAGTGGCATTCAGCCCCTGGACGCTAGAGATGGCCAACTGAAAAGCAACCTAAA--AA------------------------------------------------CAATC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:3299040-3299166 +	TAAGGAACACTTTTTGGCC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT----GTTTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA------------------------------------------------ACAATT
droSim1	chr3L:2834561-2834687 +	TAAAGAACACTTTTTGGCC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT----GTTTTGCCTAATCGCATTCAATTTCTGCACGGTAGAGATGGTACGCTTAGAAACAACCTAAA------------------------------------------------AAAATT
droSec1	super_2:3291343-3291466 +	TAATAAACACTTTTTGGTC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT----GTTTTGCCTAATCGCATTCAATTTCTGCAG---AGAGATGGTACGCTTAGAAACAACCTACA------------------------------------------------AAAATT
droYak2	chr3L:3844747-3844864 +	TAAAGTAAA---------C--AGCTAATCAACTCCATCGTGCAGAAGTTTGAGTGTCCTGT----GTGTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA------------------------------------------------ATGAGT
droEre2	scaffold_4784:5981989-5982116 +	AAGGAATACACTTTTGTCC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGT----GTGTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA------------------------------------------------GCAAGT
droAna3	scaffold_13337:7606422-7606539 +	TGAAGGATGTTTTTTGAGA--AGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCTAAT-----TTTTAACCATTCGCATTCAACCTTTGGACGGTAGAGATGGTCAGTGAGAAAGCAACCTA--------------------------------------------------------
droWil1	scaffold_180698:10215726-10215851 +	ATTCAAATACTTTTGCGTTAAGGTTGGCTGGCTCCATCGTGCTTAGGTTTGAGTGTCTT-CGTTTGTTTTCTCTAATGGCATTCAACCTTGGAGCGATAGAGACGGCCAATCGAGAAACAGCCTAAA------------------------------------------------------
droVir3	scaffold_12758:855562-855687 -	TATGTATGGATCTCTCATC--AGTTAGCTAGCTCCATCGTGCACAGGTTTGAGTGTT-TGA----GTTTTTCCTAGTGGCATTCAACCTTTGAACGGTAGAGATGGCCAACTGAAAAGCGACCTAAA------------------------------------------------CTAATA
droMoj3	scaffold_6680:1909563-1909732 -	TCAGGTATCCAATATG-----GGTTAGCGAGCTCCATCGTGCACAGGTTTGAGTGTT-TGT----GT-TTGGCTAGTCGCATTCAGCCTTTGAACGGTAGAGATGGCCAACTGAAAAGCGACCTAACTGAAAGCGAATCAAGGGAACTAGGCCAATAGGCGAGAATCATATAGAAATAGTT
droGri2	scaffold_15110:657067-657177 +	TAAAG-----------------GTTGGCGAACTCCATCGTGCACGGGTTTGAGTGTC-TGA----GT-TTGCCAAGTGGCATTCAGCCCCTGGACGCTAGAGATGGCCAACTGAAAAGCAACCTAAA-----------------------------------------------AACAATC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TAAAGAACACTTTTTGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTGTTTTGCCTAATCGCATTCAATTTCTGCACGGTAGAGATGGTACGCTTAGAAACAACCTAAA--AAAATT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
................................CATCGTGCAGAGGTTTGAGTGTC..........................................................................	23	1	395.00	395	395
................................CATCGTGCAGAGGTTTGAGTGT...........................................................................	22	1	84.00	84	84
................................CATCGTGCAGAGGTTTGAGTG............................................................................	21	1	60.00	60	60
.................................ATCGTGCAGAGGTTTGAGTGTC..........................................................................	22	1	29.00	29	29
.........................................................................CATTCAATTTCTGCACGGTAGA..................................	22	1	17.00	17	17
..............TGGCCAGCTAATCAACTCC................................................................................................	19	1	8.00	8	8
.................................ATCGTGCAGAGGTTTGAGTGTCC.........................................................................	23	1	6.00	6	6
.................................ATCGTGCAGAGGTTTGAGTGT...........................................................................	21	1	4.00	4	4
................................CATCGTGCAGAGGTTTGAGT.............................................................................	20	1	3.00	3	3
.................................ATCGTGCAGAGGTTTGAGTGTCCTG.......................................................................	25	1	2.00	2	2
.............TTGGCCAGCTAATCAACTC.................................................................................................	19	1	1.00	1	1
.................................ATCGTGCAGAGGTTTGAGTGTCCT........................................................................	24	1	1.00	1	1
..........................................................................ATTCAATTTCTGCACGGTAGA..................................	21	1	1.00	1	1

dp4

AA----------TTTAAAAAAATGAATAAATTCAAATGACAAAAATGTAAATGAATTAAA--------AAATAAATTCAAATGATAAAAAGTAAA----------TGAATAAAAAAATAAAGTAAAATT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

-27.3	-27.3	-27.3	-27.0	-27.0	-27.0

droSim1

-34.0	-34.0	-34.0	-33.7	-33.7	-33.7

droSec1

-25.1	-25.1	-25.1	-24.8	-24.8	-24.8

droYak2

-27.7	-27.7	-27.7	-27.4	-27.4	-27.4

droEre2

-27.9	-27.9	-27.9	-27.7	-27.7	-27.7

droAna3

-31.8	-31.8	-31.8	-31.7	-31.7	-31.7

dp4

-4.0	-3.5	-3.5	-3.5	-3.4	-3.3

droPer1

No secondary structure predictions returned

droWil1

-40.0	-40.0	-40.0	-39.9	-39.9	-39.9

droVir3

-34.9	-34.9	-34.9	-34.4	-34.4	-34.4

droMoj3

-27.0	-27.0	-27.0	-26.6	-26.6	-26.6

droGri2

-34.6	-34.6	-34.6	-34.2

Generated: 01/05/2013 at 05:31 PM