Secondary structure and small RNA-seq evidence for dme-mir-999

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:17623934-17624068 -	GATG--AAC---GGAG-AAG--------AA--------AGGAT-G-CCGCTCAATTACCCCGACATAGTCATACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCC----CAGCCACA-CAGCCCAGTATCAA
droSim1	chr3R:17429586-17429720 -	GATG--AAC---GGAG-AAG--------AA--------AGGAT-G-CCGCTCAATTACCCCGACATAGTCGTACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCC----CAGCCACA-CAGCCCAGTATCAA
droSec1	super_0:17996302-17996436 -	GATG--AAC---GGAG-AAG--------AA--------AGGAT-G-CCGCTCAATTACCCCGACATAGTCATACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCC----CAGCCACA-CAGCCCAGTATCAA
droYak2	chr3R:18443923-18444058 -	AA-----AT---CGAG-AAG--------AA--------AGGAT-G-CCGCTCAATTACCCCGACATAGTCATACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCCACACCAGCCACATCAGCC--ACATCGG
droEre2	scaffold_4820:10463202-10463335 +	GATG--AAC---GAAG-AAG--------AA--------AGGAT-G-CCGCTCAATTACCCCGACATAGTCATACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCC----CAGCCACACCAGCC--ACACCAG
droAna3	scaffold_13340:8622498-8622632 -	GTTGCCAAA---GGACCAAA--------AA--------AGGAT-G-CCGCTCAATTACCCCGACATAGTCGTACGGTGAATGTTGTGTATTGGAAAGCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCT-----AGCCTAC-CATCTCACTATC--
dp4	chr2:6480711-6480794 -	---------------------------------------------------------------CATAGTCGTACGGTGAATGTTGTGTATTGG--ACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGTCAGCC----AAGCAGCA--AGCC---------
droPer1	super_0:306015-306135 -	GATG----TGAAGGAG-CCC--------AA--------AGGAT-GCCCGCTCAATTACCATGACATAGTCGTACGGTGAATGTTGTGTATTGG--ACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGTCAGCC----AAGCAGCA---------------
droWil1	scaffold_181130:11672712-11672848 -	GACG--A-C---GA-CGACGACGCCAACGACAGCAGCAAAGATGTCCCGCTCAATTACCATGACATAGTCGTACGGTGAATGTTGTTTA-TGGAGTCCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCC----AAACAACA---------------
droVir3	scaffold_12822:3936742-3936840 -	G---------------------------------------------CCGCTCAATTACCGTGACATAGTCGTACGGTGAATGTTGTGTA-TGGAGTCCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGTTAGCT----AATCAACA---------------
droMoj3	scaffold_6540:17209641-17209764 -	ATTA--AAA---GG-G-CAG--------TG--------A-GTC-G-CCGCTCAATTACCGTGACATAGTCGTACGGTGAATGTTGTTTA-TGGAGTCCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTG-CAGCC----AAACAACA-GCGACC--------
droGri2	scaffold_8129:786-906 -	GATA----A---GGACAAGA--------GAC-------A-GCA-G-TCGCTCAATTACCATGACATAGTCGTACGGTGAATGTTGTGT-TTGGAGTCCAATGTTAACTGTAAGACTGTGTCTTGGTGGTTGCCAGCC----AAGCAACA-AA------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:17623934-17624068 -	GATG--AAC---GGAG-AAG--------AA--------AGGAT-G-CCGCTCAATTACCCCGACATAGTCATACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCC----CAGCCACA-CAGCCCAGTATCAA
droSim1	chr3R:17429586-17429720 -	GATG--AAC---GGAG-AAG--------AA--------AGGAT-G-CCGCTCAATTACCCCGACATAGTCGTACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCC----CAGCCACA-CAGCCCAGTATCAA
droSec1	super_0:17996302-17996436 -	GATG--AAC---GGAG-AAG--------AA--------AGGAT-G-CCGCTCAATTACCCCGACATAGTCATACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCC----CAGCCACA-CAGCCCAGTATCAA
droYak2	chr3R:18443923-18444058 -	AA-----AT---CGAG-AAG--------AA--------AGGAT-G-CCGCTCAATTACCCCGACATAGTCATACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCCACACCAGCCACATCAGCC--ACATCGG
droEre2	scaffold_4820:10463202-10463335 +	GATG--AAC---GAAG-AAG--------AA--------AGGAT-G-CCGCTCAATTACCCCGACATAGTCATACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCC----CAGCCACACCAGCC--ACACCAG
droAna3	scaffold_13340:8622498-8622632 -	GTTGCCAAA---GGACCAAA--------AA--------AGGAT-G-CCGCTCAATTACCCCGACATAGTCGTACGGTGAATGTTGTGTATTGGAAAGCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCT-----AGCCTAC-CATCTCACTATC--
dp4	chr2:6480711-6480794 -	---------------------------------------------------------------CATAGTCGTACGGTGAATGTTGTGTATTGG--ACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGTCAGCC----AAGCAGCA--AGCC---------
droPer1	super_0:306015-306135 -	GATG----TGAAGGAG-CCC--------AA--------AGGAT-GCCCGCTCAATTACCATGACATAGTCGTACGGTGAATGTTGTGTATTGG--ACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGTCAGCC----AAGCAGCA---------------
droWil1	scaffold_181130:11672712-11672848 -	GACG--A-C---GA-CGACGACGCCAACGACAGCAGCAAAGATGTCCCGCTCAATTACCATGACATAGTCGTACGGTGAATGTTGTTTA-TGGAGTCCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCC----AAACAACA---------------
droVir3	scaffold_12822:3936742-3936840 -	G---------------------------------------------CCGCTCAATTACCGTGACATAGTCGTACGGTGAATGTTGTGTA-TGGAGTCCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGTTAGCT----AATCAACA---------------
droMoj3	scaffold_6540:17209641-17209764 -	ATTA--AAA---GG-G-CAG--------TG--------A-GTC-G-CCGCTCAATTACCGTGACATAGTCGTACGGTGAATGTTGTTTA-TGGAGTCCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTG-CAGCC----AAACAACA-GCGACC--------
droGri2	scaffold_8129:786-906 -	GATA----A---GGACAAGA--------GAC-------A-GCA-G-TCGCTCAATTACCATGACATAGTCGTACGGTGAATGTTGTGT-TTGGAGTCCAATGTTAACTGTAAGACTGTGTCTTGGTGGTTGCCAGCC----AAGCAACA-AA------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GATGAACGGAGAAGAAAGGATGCCGCTCAATTACCCCGACATAGTCGTACGGTGAATGTTGTGTATTGGAGACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGCCAGCCCAGCCACACAGCCCAGTATCAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
............................................................................TGTTAACTGTAAGACTGTGTCT.....................................	22	1	1276.00	1276	1276
...........................................................................ATGTTAACTGTAAGACTGTGTCT.....................................	23	1	15.00	15	15
............................................................................TGTTAACTGTAAGACTGTGTC......................................	21	1	9.00	9	9
.............................................................................GTTAACTGTAAGACTGTGTCT.....................................	21	1	8.00	8	8
......................................ACATAGTCGTACGGTGAATGTT...........................................................................	22	1	5.00	5	5
......................................ACATAGTCGTACGGTGAATGTTG..........................................................................	23	1	2.00	2	2
............................................................................TGTTAACTGTAAGACTGTGT.......................................	20	1	2.00	2	2
...................ATGCCGCTCAATTACCCCG.................................................................................................	19	1	1.00	1	1
............................................................................TGTTAACTGTAAGACTGTGTCTC....................................	23	1	1.00	1	1

dp4

---------------------------------------CATAGTCGTACGGTGAATGTTGTGTATTGG--ACCAATGTTAACTGTAAGACTGTGTCTCGGTGGTTGTCAGCCAAGCAGCA-AGCC---------	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
............................................................................TGTTAACTGTAAGACTGTGTCT.....................................	22	1	18813.00	18813	3464	15349
............................................................................TGTTAACTGTAAGACTGTGTC......................................	21	1	1388.00	1388	132	1256
............................................................................TGTTAACTGTAAGACTGTGT.......................................	20	1	650.00	650	34	616
...........................................................................ATGTTAACTGTAAGACTGTGTCT.....................................	23	1	58.00	58	6	52
.............................................................................GTTAACTGTAAGACTGTGTCT.....................................	21	1	57.00	57	16	41
............................................................................TGTTAACTGTAAGACTGTG........................................	19	1	24.00	24	2	22
............................................................................TGTTAACTGTAAGACTGTGTCTC....................................	23	1	15.00	15	8	7
..............................................................................TTAACTGTAAGACTGTGTCT.....................................	20	1	6.00	6	2	4
...............................................................................TAACTGTAAGACTGTGTCT.....................................	19	1	4.00	4	3	1
.............................................................................GTTAACTGTAAGACTGTGTC......................................	20	1	3.00	3	1	2

Secondary Structure

dm3

-39.4	-39.1	-38.8	-38.7	-38.5	-38.4

droSim1

-39.4	-39.1	-38.8	-38.7	-38.5	-38.4

droSec1

-39.4	-39.1	-38.8	-38.7	-38.5	-38.4

droYak2

-40.2	-39.9

droEre2

-39.4	-39.1	-38.8	-38.7	-38.5	-38.4

droAna3

-40.3	-40.0	-39.5	-39.4	-39.4

dp4

-24.9	-24.9	-24.7	-24.6	-24.6	-24.6

droPer1

-41.1	-40.8

droWil1

-37.6	-37.3	-36.7

droVir3

-39.3	-39.0

droMoj3

-41.4	-41.1	-40.6

droGri2

-39.4	-39.1	-38.4

Generated: 01/05/2013 at 05:37 PM