Secondary structure and small RNA-seq evidence for dme-let-7

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:18472019-18472126 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droSim1	chr2L:18160930-18161037 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droSec1	super_7:2097967-2098074 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droYak2	chr2R:4988819-4988926 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droEre2	scaffold_4845:5799401-5799508 -	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droAna3	scaffold_12916:2379166-2379273 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGCAACTA-AGAATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACAATAAGCCGCATTT
dp4	chr4_group3:3635640-3635746 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTT--CAGATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCTCATTT
droPer1	super_1:5116219-5116325 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTT--CAGATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCTCATTT
droWil1	scaffold_180708:11623134-11623240 +	AAAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTATTCAATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCACA---
droVir3	scaffold_12963:18451337-18451441 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTATTTA-TAGAGCATACTATACAGCGTGCTAGCTTTCTTTGCTTGACAATAAGCCGCA---
droMoj3	scaffold_6500:6184568-6184672 -	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTTA-TAGACCATACTATACAGCGTGCTAGCTTTCTTTGCTTGACTATAAGCCGCA---
droGri2	scaffold_3792:132-239 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTATCTA-TCTAGCATACTATACAGCTTGCTAGCTTTCTTTGCTTGACTATAAGCAGCATAG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:18472019-18472126 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droSim1	chr2L:18160930-18161037 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droSec1	super_7:2097967-2098074 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droYak2	chr2R:4988819-4988926 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droEre2	scaffold_4845:5799401-5799508 -	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTA-CACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT
droAna3	scaffold_12916:2379166-2379273 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGCAACTA-AGAATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACAATAAGCCGCATTT
dp4	chr4_group3:3635640-3635746 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTT--CAGATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCTCATTT
droPer1	super_1:5116219-5116325 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTT--CAGATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCTCATTT
droWil1	scaffold_180708:11623134-11623240 +	AAAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTATTCAATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCACA---
droVir3	scaffold_12963:18451337-18451441 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTATTTA-TAGAGCATACTATACAGCGTGCTAGCTTTCTTTGCTTGACAATAAGCCGCA---
droMoj3	scaffold_6500:6184568-6184672 -	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTTA-TAGACCATACTATACAGCGTGCTAGCTTTCTTTGCTTGACTATAAGCCGCA---
droGri2	scaffold_3792:132-239 +	A-AGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTATCTA-TCTAGCATACTATACAGCTTGCTAGCTTTCTTTGCTTGACTATAAGCAGCATAG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTACACATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCATTT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.........................TGAGGTAGTAGGTTGTATAGT..............................................................	21	1	29.00	29	29
.........................TGAGGTAGTAGGTTGTATAGTA.............................................................	22	1	26.00	26	26
.........................TGAGGTAGTAGGTTGTATAG...............................................................	20	1	5.00	5	5
...............................................................CTATACAATGTGCTAGCTTTCT.......................	22	1	2.00	2	2
.........................TGAGGTAGTAGGTTGTATA................................................................	19	1	1.00	1	1
.........................TGAGGTAGTAGGTTGTAT.................................................................	18	1	1.00	1	1

dp4

AAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTACTT-CAGATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCTCATTT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.........................TGAGGTAGTAGGTTGTATAGT..............................................................	21	1	34347.00	34347	35	34312
.........................TGAGGTAGTAGGTTGTATAG...............................................................	20	1	20657.00	20657	4	20653
.........................TGAGGTAGTAGGTTGTATAGTA.............................................................	22	1	5937.00	5937	19	5918
.........................TGAGGTAGTAGGTTGTATA................................................................	19	1	851.00	851	0	851
.........................TGAGGTAGTAGGTTGTAT.................................................................	18	1	695.00	695	0	695
..........................GAGGTAGTAGGTTGTATAGT..............................................................	20	1	88.00	88	0	88
..........................GAGGTAGTAGGTTGTATAGTA.............................................................	21	1	43.00	43	0	43
..........................GAGGTAGTAGGTTGTATAG...............................................................	19	1	23.00	23	0	23
...............................................................CTATACAATGTGCTAGCTTTCT.......................	22	1	19.00	19	0	19
.........................TGAGGTAGTAGGTTGTATAGTAG............................................................	23	1	8.00	8	0	8
...............................................................CTATACAATGTGCTAGCTTTC........................	21	1	7.00	7	0	7
...........................AGGTAGTAGGTTGTATAG...............................................................	18	1	4.00	4	0	4
...........................AGGTAGTAGGTTGTATAGT..............................................................	19	1	4.00	4	0	4

Secondary Structure

dm3

-30.2	-29.5

droSim1

-30.2	-29.5

droSec1

-30.2	-29.5

droYak2

-30.2	-29.5

droEre2

-30.2	-29.5

droAna3

-30.1	-29.4	-29.2

dp4

-30.2	-29.5

droPer1

-30.2	-29.5

droWil1

-30.2	-29.7	-29.5

droVir3

-32.3	-31.9	-31.7	-31.6

droMoj3

-31.7	-31.3	-31.2	-31.1	-31.0

droGri2

-33.6	-33.0	-32.9	-32.6

Generated: 01/05/2013 at 05:04 PM