Secondary structure and small RNA-seq evidence for dme-mir-997

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:15152661-15152905 -	CAATTAA-TATGTAGTTTA---------------TGGAT-----CCTCTTTCAATGAATTTAGT----ATGCCCAAACTCGAAGGAGTTTCACC------------------------------------------------TCCATAAGAGCGACAGTC-CTGGAGAAGTTATCAGAGCCAAAAAAATTCATA-TGATGATGCATTTTCC--------GTCTCTGAAAACGTCTTCAG-CAGAAGTTGTTTTTAGCGAAGTGAAACTCATT-CGATTTTGATCATACTA-ACGA---CATTGGAT------G-CTTG-----GATCGGCA----GTTTGGTGGAATATA
droSim1	chr3R:6329088-6329350 +	CAATAAA-TATGTAGTTTTGGATACTCGCCAGTCAGGAT-----GCTCTGTCAATGAATTTAGT----ATGCCCAAACTCGAAGGAGTTTCACC------------------------------------------------TCCATAGGAGCGGCAGAC-CTGGAGAAGTTTTCAGAGCCAAAAAAATTCATA-TGATGATGCATTTTCA--------GTCTCTGAAAACTTCTTCAG-CAGAAGTTGATTTTAGCGAAGTGAAGCTCATT-CGATTTTGATCATACTA-ACGACATTTGTGGAT------G-CTTG-----GATCGGCA----GTTTGGTGGAATATT
droSec1	super_25:615309-615568 +	CAATAAA-TATGTAGTTTTAGATACTCGCCAGTCAGGAT-----GCTCTGTCAATGAATTTAGT----ATGCCCAAACTCGAAGGAGTTTCACC------------------------------------------------TCCATAGGAGCGGCAGAC-CTGGAGAAGTTTTCAGAGCCAACAAAATTCATA-TGATGATGCATTTTCA--------GTCTCTGAAAATTTCTTCAG-CAGAAGTTGATTTTAGCGAAGTGAAGCTCATT-CGATTTTGATCATACTA-A---CATTTGTGGAT------G-CTTG-----GATCGTCA----GTTTGGTGGAATATT
droYak2	chrU:8935876-8936155 -	AAAATAAAAGTTGAATTTTGAAAAATAAA--ATTTCCAA-----TTTTTGACCATGATTTTTGAACGTTTGCCGAAAATCGT----GTTTCTGCGACTATAAATATCCGTATTTTGATCATAACTTTCGAAATATTGGTCCAATCA-TGGAATGCCACAC-CTCGTTGAGTTC-----------------------GTAATTAAATTTCCAATCGAACTGTGTTTA---------AAAA-TAAAAGTTGAATTTTGAAAAATAAAATTT--CCAATTTTTGACCATG---------ATTTTTGAAC------G-TTTGCCGAAAATCG--T----GTTTCTGCGACTATA
droEre2	scaffold_4784:21223629-21223900 -	CAAGACG--------CCTTAAA-----GCGAGTTCAGCTTTACTGTTCTA-GAATGCAGTTTAT----ATACCCAAACTCGAAGGAGTTCCACA------------------------------------------------TTAAGAAGAGCAGCAGAAGCAGAAAAAAATGTCTGGACCCTTGAAATTCATTTTGCAAATGCATTTCCATT------GGCTCGGAAATCTTTCTCTGTCAGGTGTTGATTTTTTAAAAGTGGAGCTCATT-CGATTTTGAATATATAAAATAACAGTTCTTGATATGTATGAGTTG-----GATTTGCACCTTGTCTGACAGAAAAAC
droAna3	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:15152661-15152905 -	CAATTAATATGTAGTTTA---------------TGGATCCTCTTT----CAATGAATTTAGTATGCCCAAACTCGAAGGAGTTTCACCTCCATAAGAGCGACAGTC-CTGGAGAAGTTATCAGAGCCAAAAAAATTCATA-TGATGATGCATTTTCC--GTCTCTGAAAACGTCTTCAG-CAGAAGTTGTTTTTAGCGAAGTGAAACTCATTCGATTTTGATCATACTA-ACGACAT---TGGATG-------CTTGGATCGGCA----GTTTGGTGGAATATA
droSim1	chr3R:6329088-6329350 +	CAATAAATATGTAGTTTTGGATACTCGCCAGTCAGGATGCTCTGT----CAATGAATTTAGTATGCCCAAACTCGAAGGAGTTTCACCTCCATAGGAGCGGCAGAC-CTGGAGAAGTTTTCAGAGCCAAAAAAATTCATA-TGATGATGCATTTTCA--GTCTCTGAAAACTTCTTCAG-CAGAAGTTGATTTTAGCGAAGTGAAGCTCATTCGATTTTGATCATACTA-ACGACATTTGTGGATG-------CTTGGATCGGCA----GTTTGGTGGAATATT
droSec1	super_25:615309-615568 +	CAATAAATATGTAGTTTTAGATACTCGCCAGTCAGGATGCTCTGT----CAATGAATTTAGTATGCCCAAACTCGAAGGAGTTTCACCTCCATAGGAGCGGCAGAC-CTGGAGAAGTTTTCAGAGCCAACAAAATTCATA-TGATGATGCATTTTCA--GTCTCTGAAAATTTCTTCAG-CAGAAGTTGATTTTAGCGAAGTGAAGCTCATTCGATTTTGATCATACTA-A---CATTTGTGGATG-------CTTGGATCGTCA----GTTTGGTGGAATATT
droEre2	scaffold_4784:21223629-21223900 -	CAAGAC-------GCCTTAAA-----GCGAGTTCAGCTTTACTGTTCTAGAATGCAGTTTATATACCCAAACTCGAAGGAGTTCCACATTAAGAAGAGCAGCAGAAGCAGAAAAAAATGTCTGGACCCTTGAAATTCATTTTGCAAATGCATTTCCATTGGCTCGGAAATCTTTCTCTGTCAGGTGTTGATTTTTTAAAAGTGGAGCTCATTCGATTTTGAATATATAAAATAACAGTTCTTGATATGTATGAGTTGGATTTGCACCTTGTCTGACAGAAAAAC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CAATAAATATGTAGTTTTGGATACTCGCCAGTCAGGATGCTCTGTCAATGAATTTAGTATGCCCAAACTCGAAGGAGTTTCACCTCCATAGGAGCGGCAGACCTGGAGAAGTTTTCAGAGCCAAAAAAATTCATATGATGATGCATTTTCAGTCTCTGAAAACTTCTTCAGCAGAAGTTGATTTTAGCGAAGTGAAGCTCATTCGATTTTGATCATACTAACGACATTTGTGGATGCTTGGATCGGCAGTTTGGTGGAATATT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

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

Secondary Structure

dm3

-76.5	-76.1	-75.9	-75.5

droSim1

-77.8	-77.8	-77.7	-77.7	-77.6	-77.6

droSec1

-72.6	-72.5	-72.0	-71.9	-71.7

droYak2

-44.9	-44.9	-44.8	-44.8	-44.5	-44.5

droEre2

-78.7	-78.7	-78.5	-78.5	-78.2	-78.2

droAna3

No secondary structure predictions returned

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 01/05/2013 at 05:36 PM